Vlf/elf radiation patterns of arbitrarily oriented electric and magnetic dipoles in a cold lossless multicomponent magnetoplasma.

NASA Technical Reports Server (NTRS)

Wang, T. N. C.; Bell, T. F.

1972-01-01

With the use of a power integral formulation, a study is made of the vlf/elf radiation patterns of arbitrarily oriented electric and magnetic dipoles in a cold lossless multicomponent magnetoplasma. Expressions for the ray patterns are initially developed that apply for arbitrary values of driving frequency, static magnetic-field strength, plasma density, and composition. These expressions are subsequently specialized to vlf/elf radiation in a plasma modeled on the magnetosphere. A series of representative pattern plots are presented for frequencies between the proton and electron gyrofrequencies. These patterns illustrate the fact that focusing effects that arise from the geometrical properties of the refractive index surface tend to dominate the radiation distribution over the entire range from the electron gyrofrequency to 4.6 times the proton gyrofrequency. It is concluded that focusing effects should be of significant importance in the design of a vlf/elf satellite transmitting system in the magnetosphere.

Proposed modification of the criterion for the region of validity of the inverse-power expansion in diatomic long-range potentials

NASA Astrophysics Data System (ADS)

Ji, Bing; Tsai, Chin-Chun; Stwalley, William C.

1995-04-01

A modified internuclear distance criterion, RLR- m, as the lower bound for the region of validity of the inverse-power expansion of the diatomic long-range potential is proposed. This new criterion takes into account the spatial orientation of the atomic orbitals while retaining the simplicity of the traditional Le Roy radius, RLR for the interaction of S state atoms. Recent experimental and theoretical results for various excited states in Na 2 suggest that this proposed RLR- m is an appropriate generalization of RLR.

Start-up of electrophoresis of an arbitrarily oriented dielectric cylinder.

PubMed

Chen, Guan Y; Keh, Huan J

2014-09-01

An analytical study is presented for the transient electrophoretic response of a circular cylindrical particle to the step application of an electric field. The electric double layer adjacent to the particle surface is thin but finite compared with the radius of the particle. The time-evolving electroosmotic velocity at the outer boundary of the double layer is utilized as a slip condition so that the transient momentum conservation equation for the bulk fluid flow is solved. Explicit formulas for the unsteady electrophoretic velocity of the particle are obtained for both axially and transversely applied electric fields, and can be linearly superimposed for an arbitrarily-oriented applied field. If the cylindrical particle is neutrally buoyant in the suspending fluid, the transient electrophoretic velocity is independent of the orientation of the particle relative to the applied electric field and will be in the direction of the applied field. If the particle is different in density from the fluid, then the direction of electrophoresis will not coincide with that of the applied field until the steady state is attained. The growth of the electrophoretic mobility with the elapsed time for a cylindrical particle is substantially slower than for a spherical particle. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Decoupled Magnetoquasistatic Non-Line-of-Sight Position and Orientation Sensing for Arbitrary Distances

NASA Technical Reports Server (NTRS)

Arumugam, Darmindra D. (Inventor)

2017-01-01

Methods and systems for non-line-of-sight positioning are disclosed for arbitrarily short to long ranges, where positioning is achieved using a single anchor not requiring tri-/multi-lateration or tri-/multi-angulation. Magnetoquasistatic fields can be used to determine position and orientation of a device in two or three dimensions. Two or three axis coils can be used in receivers and transmitters. The magnetoquasistatic equations are solved in different scenarios, taking into consideration the image signals originating from the interaction between the fields and ground/earth.

Performance Analysis and Experimental Validation of the Direct Strain Imaging Method

Treesearch

Athanasios Iliopoulos; John G. Michopoulos; John C. Hermanson

2013-01-01

Direct Strain Imaging accomplishes full field measurement of the strain tensor on the surface of a deforming body, by utilizing arbitrarily oriented engineering strain measurements originating from digital imaging. In this paper an evaluation of the method’s performance with respect to its operating parameter space is presented along with a preliminary...

Material characterization in partially filled waveguides using inverse scattering and multiple sample orientations

NASA Astrophysics Data System (ADS)

Sjöberg, Daniel; Larsson, Christer

2015-06-01

We present a method aimed at reducing uncertainties and instabilities when characterizing materials in waveguide setups. The method is based on measuring the S parameters for three different orientations of a rectangular sample block in a rectangular waveguide. The corresponding geometries are modeled in a commercial full-wave simulation program, taking any material parameters as input. The material parameters of the sample are found by minimizing the squared distance between measured and calculated S parameters. The information added by the different sample orientations is quantified using the Cramér-Rao lower bound. The flexibility of the method allows the determination of material parameters of an arbitrarily shaped sample that fits in the waveguide.

Spectral Analysis of Two Coupled Diatomic Rotor Molecules

PubMed Central

Crogman, Horace T.; Harter, William G.

2014-01-01

In a previous article the theory of frame transformation relation between Body Oriented Angular (BOA) states and Lab Weakly Coupled states (LWC) was developed to investigate simple rotor–rotor interactions. By analyzing the quantum spectrum for two coupled diatomic molecules and comparing it with spectrum and probability distribution of simple models, evidence was found that, as we move from a LWC state to a strongly coupled state, a single rotor emerges in the strong limit. In the low coupling, the spectrum was quadratic which indicates the degree of floppiness in the rotor–rotor system. However in the high coupling behavior it was found that the spectrum was linear which corresponds to a rotor deep in a well. PMID:25353181

High-precision control of static magnetic field magnitude, orientation, and gradient using optically pumped vapour cell magnetometry.

PubMed

Ingleby, S J; Griffin, P F; Arnold, A S; Chouliara, M; Riis, E

2017-04-01

An integrated system of hardware and software allowing precise definition of arbitrarily oriented magnetic fields up to |B| = 1 μT within a five-layer Mumetal shield is described. The system is calibrated with reference to magnetic resonance observed between Zeeman states of the 6S 1/2 F = 4 133 Cs ground state. Magnetic field definition over the full 4π solid angle is demonstrated with one-sigma tolerances in magnitude, orientation, and gradient of δ|B| = 0.94 nT, δθ = 5.9 mrad, and δ|∇B|=13.0 pT/mm, respectively. This field control is used to empirically map M x magnetometer signal amplitude as a function of the static field (B 0 ) orientation.

Robust computation of dipole electromagnetic fields in arbitrarily anisotropic, planar-stratified environments.

PubMed

Sainath, Kamalesh; Teixeira, Fernando L; Donderici, Burkay

2014-01-01

We develop a general-purpose formulation, based on two-dimensional spectral integrals, for computing electromagnetic fields produced by arbitrarily oriented dipoles in planar-stratified environments, where each layer may exhibit arbitrary and independent anisotropy in both its (complex) permittivity and permeability tensors. Among the salient features of our formulation are (i) computation of eigenmodes (characteristic plane waves) supported in arbitrarily anisotropic media in a numerically robust fashion, (ii) implementation of an hp-adaptive refinement for the numerical integration to evaluate the radiation and weakly evanescent spectra contributions, and (iii) development of an adaptive extension of an integral convergence acceleration technique to compute the strongly evanescent spectrum contribution. While other semianalytic techniques exist to solve this problem, none have full applicability to media exhibiting arbitrary double anisotropies in each layer, where one must account for the whole range of possible phenomena (e.g., mode coupling at interfaces and nonreciprocal mode propagation). Brute-force numerical methods can tackle this problem but only at a much higher computational cost. The present formulation provides an efficient and robust technique for field computation in arbitrary planar-stratified environments. We demonstrate the formulation for a number of problems related to geophysical exploration.

AK-cut crystal resonators

NASA Technical Reports Server (NTRS)

Kahan, A.; Euler, F. K.

1983-01-01

Calculations have predicted the existence of crystallographically doubly rotated quartz orientations with turnover temperatures which are considerably less sensitive to angular misorientation then comparable AT- or BT-cuts. These crystals are arbitrarily designated as the AK-cut. Experimental data is given for seven orientations, phi-angle variations between 30-46 deg and theta-angle variations between 21-28 deg measured on 3.3-3.4 MHz fundamental mode resonators vibrating in the thickness shear c-mode. The experimental turnover temperatures of these resonators are between 80 C and 150 C, in general agreement with calculated values. The normalized frequency change as a function of temperature has been fitted with a cubic equation.

Strong-field approximation for ionization of a diatomic molecule by a strong laser field. II. The role of electron rescattering off the molecular centers

NASA Astrophysics Data System (ADS)

Busuladžić, M.; Gazibegović-Busuladžić, A.; Milošević, D. B.; Becker, W.

2008-09-01

The strong-field approximation for ionization of diatomic molecules by a strong laser field [D. B. Milošević, Phys. Rev. A 74, 063404 (2006)] is generalized to include rescattering of the ionized electron wave packet off the molecular centers (the electron’s parent ion or the second atom). There are four rescattering contributions to the ionization rate, which are responsible for the high-energy plateau in the electron spectra and which interfere in a complicated manner. The spectra are even more complicated due to the different symmetry properties of the atomic orbitals of which a particular molecular orbital consists. Nevertheless, a comparatively simple condition emerges for the destructive interference of all these contributions, which yields a curve in the (Epf,θ) plane. Here θ is the electron emission angle and Epf is the electron kinetic energy. The resulting suppression of the rescattering plateau can be strong and affect a large area of the (Epf,θ) plane, depending on the orientation of the molecule. We illustrate this using the examples of the 3σg molecular orbital of N2 and the 1πg molecular orbital of O2 for various orientations of these molecules with respect to the laser polarization axis. For N2 , for perpendicular orientation and the equilibrium internuclear distance R0 , we find that the minima of the ionization rate form the curve Epfcos2θ=π2/(2R02) in the (Epf,θ) plane. For O2 the rescattering plateau is absent for perpendicular orientation.

Connection between the two branches of the quantum two-stream instability across the k space

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bret, A.; Haas, F.

2010-05-15

The stability of two quantum counterstreaming electron beams is investigated within the quantum plasma fluid equations for arbitrarily oriented wave vectors k. The analysis reveals that the two quantum two-stream unstable branches are indeed connected by a continuum of unstable modes with oblique wave vectors. Using the longitudinal approximation, the stability domain for any k is analytically explained, together with the growth rate.

Effect of Ply Orientation and Crack Location on SIFs in Finite Multilayers with Aligned Cracks

NASA Astrophysics Data System (ADS)

Chen, Linfeng; Pindera, Marek-Jerzy

2008-02-01

An exact elasticity solution is presented for arbitrarily laminated finite multilayers in a state of generalized plane deformation under horizontally pinned end constraints that are weakened by aligned cracks. Based on half-range Fourier series and the local/global stiffness matrix approach, the mixed boundary-value problem is reduced to Cauchy-type singular integral equations in the unknown displacement discontinuities. Solution to these equations is obtained using the approach developed by Erdogan and co-workers. Numerical results quantify the thus-far undocumented geometric and material effects on Mode I, II and III stress intensity factors in composite multilayers with interacting cracks under uniform vertical displacement. These effects include finite dimensions, crack location, material anisotropy due to a unidirectional fiber-reinforced layer/s orientation, and orientational grading.

Depolarization and Scattering of Electromagnetic Waves. Appendices.

DTIC Science & Technology

1986-06-30

for both specular point scattering and Bragg scattering in a self-consistent manner is used to express the total cross section of the flake as a...by Arbitrarily Oriented Composite Rough Surfaces. In this work the full wave approach is used to determine the modu- lations of the like and cross...analyze multiple scattering using the equation of radiative transfer with the general Stokes’ parameters. Our ultimate goal is to develop codes which will

Equilibrium intermediate-state patterns in a type-I superconducting slab in an arbitrarily oriented applied magnetic field

DOE PAGES

Clem, John; Prozorov, Ruslan; Wijngaarden, Rinke J.

2013-09-04

The equilibrium topology of superconducting and normal domains in flat type-I superconductors is investigated. Important improvements with respect to previous work are that (1) the energy of the external magnetic field, as deformed by the presence of superconducting domains, is calculated in the same way for three different topologies and (2) calculations are made for arbitrary orientation of the applied field. A phase diagram is presented for the minimum-energy topology as a function of applied field magnitude and angle. For small (large) applied fields, normal (superconducting) tubes are found, while for intermediate fields, parallel domains have a lower energy. Themore » range of field magnitudes for which the superconducting-tubes structure is favored shrinks when the field is more in-plane oriented.« less

Vector solution for the mean electromagnetic fields in a layer of random particles

NASA Technical Reports Server (NTRS)

Lang, R. H.; Seker, S. S.; Levine, D. M.

1986-01-01

The mean electromagnetic fields are found in a layer of randomly oriented particles lying over a half space. A matrix-dyadic formulation of Maxwell's equations is employed in conjunction with the Foldy-Lax approximation to obtain equations for the mean fields. A two variable perturbation procedure, valid in the limit of small fractional volume, is then used to derive uncoupled equations for the slowly varying amplitudes of the mean wave. These equations are solved to obtain explicit expressions for the mean electromagnetic fields in the slab region in the general case of arbitrarily oriented particles and arbitrary polarization of the incident radiation. Numerical examples are given for the application to remote sensing of vegetation.

Proceedings of the Annual DARPA/AFGL Seismic Research Symposium (7th) Held in Colorado Springs, Colorado on 6-8 May 1985

DTIC Science & Technology

1990-11-08

seismograms were calculated for the three fundemental sources needed to construct an arbitrarily oriented dislocation or deviatoric moment tensor...or the first motion approximation method(FMA). Vertical and radial displacements for the three fundemental source terms are shown since each source...significantly interfere with the SV body wave to produce varying levels of distortion of the waveform among the three fundemental sources. Note, for example

Nonlinear Finite Element Analysis of Sandwich Composites.

DTIC Science & Technology

1981-03-01

to the element midsurface z - z(x,y) at all points. An additional coordinate r is used to describe the distance away from the midsurface at any point...It is assumed that on the element level, the shell is shallow, so that z2 2 (56) ,y everywhere. The unit vector normal to the shell midsurface at a...relations above do not involve the orientation of the displaced midsurface normal, and, therefore, apply to arbitrarily large displacements and rotations

Modeling and simulation of the deposition/relaxation processes of polycrystalline diatomic structures of metallic nitride films

NASA Astrophysics Data System (ADS)

García, M. F.; Restrepo-Parra, E.; Riaño-Rojas, J. C.

2015-05-01

This work develops a model that mimics the growth of diatomic, polycrystalline thin films by artificially splitting the growth into deposition and relaxation processes including two stages: (1) a grain-based stochastic method (grains orientation randomly chosen) is considered and by means of the Kinetic Monte Carlo method employing a non-standard version, known as Constant Time Stepping, the deposition is simulated. The adsorption of adatoms is accepted or rejected depending on the neighborhood conditions; furthermore, the desorption process is not included in the simulation and (2) the Monte Carlo method combined with the metropolis algorithm is used to simulate the diffusion. The model was developed by accounting for parameters that determine the morphology of the film, such as the growth temperature, the interacting atomic species, the binding energy and the material crystal structure. The modeled samples exhibited an FCC structure with grain formation with orientations in the family planes of < 111 >, < 200 > and < 220 >. The grain size and film roughness were analyzed. By construction, the grain size decreased, and the roughness increased, as the growth temperature increased. Although, during the growth process of real materials, the deposition and relaxation occurs simultaneously, this method may perhaps be valid to build realistic polycrystalline samples.

Diatomic Metasurface for Vectorial Holography.

PubMed

Deng, Zi-Lan; Deng, Junhong; Zhuang, Xin; Wang, Shuai; Li, Kingfai; Wang, Yao; Chi, Yihui; Ye, Xuan; Xu, Jian; Wang, Guo Ping; Zhao, Rongkuo; Wang, Xiaolei; Cao, Yaoyu; Cheng, Xing; Li, Guixin; Li, Xiangping

2018-05-09

The emerging metasurfaces with the exceptional capability of manipulating an arbitrary wavefront have revived the holography with unprecedented prospects. However, most of the reported metaholograms suffer from limited polarization controls for a restrained bandwidth in addition to their complicated meta-atom designs with spatially variant dimensions. Here, we demonstrate a new concept of vectorial holography based on diatomic metasurfaces consisting of metamolecules formed by two orthogonal meta-atoms. On the basis of a simply linear relationship between phase and polarization modulations with displacements and orientations of identical meta-atoms, active diffraction of multiple polarization states and reconstruction of holographic images are simultaneously achieved, which is robust against both incident angles and wavelengths. Leveraging this appealing feature, broadband vectorial holographic images with spatially varying polarization states and dual-way polarization switching functionalities have been demonstrated, suggesting a new route to achromatic diffractive elements, polarization optics, and ultrasecure anticounterfeiting.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aagesen, Larry K.; Thornton, Katsuyo, E-mail: kthorn@umich.edu; Coltrin, Michael E.

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. The model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. The model provides a route to optimize masks and processing conditions during materialsmore » synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

Mathematical model of solar radiation based on climatological data from NASA SSE

NASA Astrophysics Data System (ADS)

Obukhov, S. G.; Plotnikov, I. A.; Masolov, V. G.

2018-05-01

An original model of solar radiation arriving at the arbitrarily oriented surface has been developed. The peculiarity of the model is that it uses numerical values of the atmospheric transparency index and the surface albedo from the NASA SSE database as initial data. The model is developed in the MatLab/Simulink environment to predict the main characteristics of solar radiation for any geographical point in Russia, including those for territories with no regular actinometric observations.

Quantum angular momentum diffusion of rigid bodies

NASA Astrophysics Data System (ADS)

Papendell, Birthe; Stickler, Benjamin A.; Hornberger, Klaus

2017-12-01

We show how to describe the diffusion of the quantized angular momentum vector of an arbitrarily shaped rigid rotor as induced by its collisional interaction with an environment. We present the general form of the Lindblad-type master equation and relate it to the orientational decoherence of an asymmetric nanoparticle in the limit of small anisotropies. The corresponding diffusion coefficients are derived for gas particles scattering off large molecules and for ambient photons scattering off dielectric particles, using the elastic scattering amplitudes.

Novel sex cells and evidence for sex pheromones in diatoms.

PubMed

Sato, Shinya; Beakes, Gordon; Idei, Masahiko; Nagumo, Tamotsu; Mann, David G

2011-01-01

Diatoms belong to the stramenopiles, one of the largest groups of eukaryotes, which are primarily characterized by a presence of an anterior flagellum with tubular mastigonemes and usually a second, smooth flagellum. Based on cell wall morphology, diatoms have historically been divided into centrics and pennates, of which only the former have flagella and only on the sperm. Molecular phylogenies show the pennates to have evolved from among the centrics. However, the timing of flagellum loss--whether before the evolution of the pennate lineage or after--is unknown, because sexual reproduction has been so little studied in the 'araphid' basal pennate lineages, to which Pseudostaurosira belongs. Sexual reproduction of an araphid pennate, Pseudostaurosira trainorii, was studied with light microscopy (including time lapse observations and immunofluorescence staining observed under confocal scanning laser microscopy) and SEM. We show that the species produces motile male gametes. Motility is mostly associated with the extrusion and retrieval of microtubule-based 'threads', which are structures hitherto unknown in stramenopiles, their number varying from one to three per cell. We also report experimental evidence for sex pheromones that reciprocally stimulate sexualization of compatible clones and orientate motility of the male gametes after an initial 'random walk'. The threads superficially resemble flagella, in that both are produced by male gametes and contain microtubules. However, one striking difference is that threads cannot beat or undulate and have no motility of their own, and they do not bear mastigonemes. Threads are sticky and catch and draw objects, including eggs. The motility conferred by the threads is probably crucial for sexual reproduction of P. trainorii, because this diatom is non-motile in its vegetative stage but obligately outbreeding. Our pheromone experiments are the first studies in which gametogenesis has been induced in diatoms by cell-free exudates, opening new possibilities for molecular 'dissection' of sexualization.

A multi-agent quantum Monte Carlo model for charge transport: Application to organic field-effect transistors

NASA Astrophysics Data System (ADS)

Bauer, Thilo; Jäger, Christof M.; Jordan, Meredith J. T.; Clark, Timothy

2015-07-01

We have developed a multi-agent quantum Monte Carlo model to describe the spatial dynamics of multiple majority charge carriers during conduction of electric current in the channel of organic field-effect transistors. The charge carriers are treated by a neglect of diatomic differential overlap Hamiltonian using a lattice of hydrogen-like basis functions. The local ionization energy and local electron affinity defined previously map the bulk structure of the transistor channel to external potentials for the simulations of electron- and hole-conduction, respectively. The model is designed without a specific charge-transport mechanism like hopping- or band-transport in mind and does not arbitrarily localize charge. An electrode model allows dynamic injection and depletion of charge carriers according to source-drain voltage. The field-effect is modeled by using the source-gate voltage in a Metropolis-like acceptance criterion. Although the current cannot be calculated because the simulations have no time axis, using the number of Monte Carlo moves as pseudo-time gives results that resemble experimental I/V curves.

A multi-agent quantum Monte Carlo model for charge transport: Application to organic field-effect transistors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bauer, Thilo; Jäger, Christof M.; Jordan, Meredith J. T.

2015-07-28

We have developed a multi-agent quantum Monte Carlo model to describe the spatial dynamics of multiple majority charge carriers during conduction of electric current in the channel of organic field-effect transistors. The charge carriers are treated by a neglect of diatomic differential overlap Hamiltonian using a lattice of hydrogen-like basis functions. The local ionization energy and local electron affinity defined previously map the bulk structure of the transistor channel to external potentials for the simulations of electron- and hole-conduction, respectively. The model is designed without a specific charge-transport mechanism like hopping- or band-transport in mind and does not arbitrarily localizemore » charge. An electrode model allows dynamic injection and depletion of charge carriers according to source-drain voltage. The field-effect is modeled by using the source-gate voltage in a Metropolis-like acceptance criterion. Although the current cannot be calculated because the simulations have no time axis, using the number of Monte Carlo moves as pseudo-time gives results that resemble experimental I/V curves.« less

Field-free orientation of diatomic molecule via the linearly polarized resonant pulses

NASA Astrophysics Data System (ADS)

Li, Su-Yu; Guo, Fu-Ming; Wang, Jun; Yang, Yu-Jun; Jin, Ming-Xing

2015-10-01

We propose a scheme to coherently control the field-free orientation of NO molecule whose rotational temperature is above 0 K. It is found that the maximum molecular orientation is affected by two factors: one is the sum of the population of M = 0 rotational states and the other is their distribution, however, their distribution plays a much more significant role in molecular orientation than the sum of their population. By adopting a series of linearly polarized pulses resonant with the rotational states, the distribution of M = 0 rotational states is well rearranged. Though the number of pulses used is small, a relatively high orientation degree can be obtained. This scheme provides a promising approach to the achievement of a good orientation effect. Project supported by the National Basic Research Program of China (Grant No. 2013CB922200), the National Natural Science Foundation of China (Grant Nos. 11034003, 11474129, 11274141, and 11304116), the Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20130061110021), and the Graduate Innovation Fund of Jilin University (Grant No. 2015091).

A generalized crystal-cutting method for modeling arbitrarily oriented crystals in 3D periodic simulation cells with applications to crystal-crystal interfaces

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew P.; Mathew, Nithin; Jiang, Shan; Sewell, Thomas D.

2016-10-01

A Generalized Crystal-Cutting Method (GCCM) is developed that automates construction of three-dimensionally periodic simulation cells containing arbitrarily oriented single crystals and thin films, two-dimensionally (2D) infinite crystal-crystal homophase and heterophase interfaces, and nanostructures with intrinsic N-fold interfaces. The GCCM is based on a simple mathematical formalism that facilitates easy definition of constraints on cut crystal geometries. The method preserves the translational symmetry of all Bravais lattices and thus can be applied to any crystal described by such a lattice including complicated, low-symmetry molecular crystals. Implementations are presented with carefully articulated combinations of loop searches and constraints that drastically reduce computational complexity compared to simple loop searches. Orthorhombic representations of monoclinic and triclinic crystals found using the GCCM overcome some limitations in standard distributions of popular molecular dynamics software packages. Stability of grain boundaries in β-HMX was investigated using molecular dynamics and molecular statics simulations with 2D infinite crystal-crystal homophase interfaces created using the GCCM. The order of stabilities for the four grain boundaries studied is predicted to correlate with the relative prominence of particular crystal faces in lab-grown β-HMX crystals. We demonstrate how nanostructures can be constructed through simple constraints applied in the GCCM framework. Example GCCM constructions are shown that are relevant to some current problems in materials science, including shock sensitivity of explosives, layered electronic devices, and pharmaceuticals.

Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

PubMed Central

Yuan, Kai-Jun; Bandrauk, André D.

2015-01-01

We present molecular photoionization processes by intense attosecond ultraviolet laser pulses from numerical solutions of time-dependent Schrödinger equations. Simulations preformed on a single electron diatomic H2+ show minima in molecular photoelectron energy spectra resulting from two center interference effects which depend strongly on molecular alignment. We attribute such sensitivity to the spatial orientation asymmetry of the photoionization process from the two nuclei. A similar influence on photoelectron kinetic energies is also presented. PMID:26798785

Real time en face Fourier-domain optical coherence tomography with direct hardware frequency demodulation

PubMed Central

Biedermann, Benjamin R.; Wieser, Wolfgang; Eigenwillig, Christoph M.; Palte, Gesa; Adler, Desmond C.; Srinivasan, Vivek J.; Fujimoto, James G.; Huber, Robert

2009-01-01

We demonstrate en face swept source optical coherence tomography (ss-OCT) without requiring a Fourier transformation step. The electronic optical coherence tomography (OCT) interference signal from a k-space linear Fourier domain mode-locked laser is mixed with an adjustable local oscillator, yielding the analytic reflectance signal from one image depth for each frequency sweep of the laser. Furthermore, a method for arbitrarily shaping the spectral intensity profile of the laser is presented, without requiring the step of numerical apodization. In combination, these two techniques enable sampling of the in-phase and quadrature signal with a slow analog-to-digital converter and allow for real-time display of en face projections even for highest axial scan rates. Image data generated with this technique is compared to en face images extracted from a three-dimensional OCT data set. This technique can allow for real-time visualization of arbitrarily oriented en face planes for the purpose of alignment, registration, or operator-guided survey scans while simultaneously maintaining the full capability of high-speed volumetric ss-OCT functionality. PMID:18978919

Geometric Modeling of Inclusions as Ellipsoids

NASA Technical Reports Server (NTRS)

Bonacuse, Peter J.

2008-01-01

Nonmetallic inclusions in gas turbine disk alloys can have a significant detrimental impact on fatigue life. Because large inclusions that lead to anomalously low lives occur infrequently, probabilistic approaches can be utilized to avoid the excessively conservative assumption of lifing to a large inclusion in a high stress location. A prerequisite to modeling the impact of inclusions on the fatigue life distribution is a characterization of the inclusion occurrence rate and size distribution. To help facilitate this process, a geometric simulation of the inclusions was devised. To make the simulation problem tractable, the irregularly sized and shaped inclusions were modeled as arbitrarily oriented, three independent dimensioned, ellipsoids. Random orientation of the ellipsoid is accomplished through a series of three orthogonal rotations of axes. In this report, a set of mathematical models for the following parameters are described: the intercepted area of a randomly sectioned ellipsoid, the dimensions and orientation of the intercepted ellipse, the area of a randomly oriented sectioned ellipse, the depth and width of a randomly oriented sectioned ellipse, and the projected area of a randomly oriented ellipsoid. These parameters are necessary to determine an inclusion s potential to develop a propagating fatigue crack. Without these mathematical models, computationally expensive search algorithms would be required to compute these parameters.

Local fields and effective conductivity tensor of ellipsoidal particle composite with anisotropic constituents

NASA Astrophysics Data System (ADS)

Kushch, Volodymyr I.; Sevostianov, Igor; Giraud, Albert

2017-11-01

An accurate semi-analytical solution of the conductivity problem for a composite with anisotropic matrix and arbitrarily oriented anisotropic ellipsoidal inhomogeneities has been obtained. The developed approach combines the superposition principle with the multipole expansion of perturbation fields of inhomogeneities in terms of ellipsoidal harmonics and reduces the boundary value problem to an infinite system of linear algebraic equations for the induced multipole moments of inhomogeneities. A complete full-field solution is obtained for the multi-particle models comprising inhomogeneities of diverse shape, size, orientation and properties which enables an adequate account for the microstructure parameters. The solution is valid for the general-type anisotropy of constituents and arbitrary orientation of the orthotropy axes. The effective conductivity tensor of the particulate composite with anisotropic constituents is evaluated in the framework of the generalized Maxwell homogenization scheme. Application of the developed method to composites with imperfect ellipsoidal interfaces is straightforward. Their incorporation yields probably the most general model of a composite that may be considered in the framework of analytical approach.

Structure and screening in molecular and metallic hydrogen at high pressure

NASA Technical Reports Server (NTRS)

Wood, D. M.; Ashcroft, N. W.

1981-01-01

A variational wavefunction is used to express the (spin restricted) Hartree-Fock energy as reciprocal lattice sums for static lattice FCC monatomic hydrogen and diatomic Pa3 molecular hydrogen. In the monatomic phase the hydrogenic orbital range closely parallels the inverse Thomas-Fermi wavevector; the corresponding energy E has a minimum of -0.929 Ryd/electron at r sub s = 1.67. For the diatomic phase E(r sub s) is similar, but the constituent energies, screening, and bond length reflect a qualitative change in the nature of the solid at r sub s = 2.8. This change is interpreted in terms of a transition from protons as structural units (at high density) to weakly interacting models (at low density). Insensitivity of the total energy to a rapid fall in the bond length suggests association with the rotational transition where the rapid molecular orientations characteristic of high pressures disappear and the molecules rotate freely at low pressure.

Phase-field simulations of GaN growth by selective area epitaxy on complex mask geometries

DOE PAGES

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung; ...

2015-05-15

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

Acoustic levitation in the presence of gravity

NASA Technical Reports Server (NTRS)

Collas, P.; Barmatz, M.; Shipley, C.

1989-01-01

The method of Gor'kov (1961) has been applied to derive general expressions for the total potential and force on a small spherical object in a resonant chamber in the presence of both acoustic and gravitational force fields. The levitation position is also determined in rectangular resonators for the simultaneous excitation of up to three acoustic modes, and the results are applied to the triple-axis acoustic levitator. The analysis is applied to rectangular, spherical, and cylindrical single-mode levitators that are arbitrarily oriented relative to the gravitational force field. Criteria are determined for isotropic force fields in rectangular and cylindrical resonators. It is demonstrated that an object will be situated within a volume of possible levitation positions at a point determined by the relative strength of the acoustic and gravitational fields and the orientation of the chamber relative to gravity.

Interannual variation in seasonal diatom dynamics - what information is preserved in an annual sediment record?

NASA Astrophysics Data System (ADS)

Maier, D. B.; Bigler, C.; Diehl, S.

2017-12-01

Diatom sediment assemblages are among the most important proxies for past climate and ecological condition reconstruction in aquatic environments, but the role of seasonality in the formation of diatom records is poorly understood. In this study we combine the diatom record of a varved sediment with year-round physico-chemical water column monitoring and the corresponding sequential sediment trap diatom record to disentangle the process information contained in a diatom sediment signal. The comparison of three consecutive annual diatom records indicates that the entire annual diatom sediment signal can be driven by winter air temperature induced timing of ice and snow melt and persistent under-ice stratification promoting an early diatom bloom under ice before spring lake over-turn. By contrast, in a year of late ice thinning when the chlorophyll a maximum occurred after spring lake over-turn, a more annually integrated diatom sediment signal was built buy a continuous diatom flux. The contrasting diatom records produced during years of different winter conditions have important implications for diatom based paleoecological reconstructions. Decadal records of sediment trap samples as well as long-term varved sediment records provide further support for the role of late winter and early spring weather conditions in determining sediment diatom assemblages.

Strong-field ionization of linear molecules by a bicircular laser field: Symmetry considerations

NASA Astrophysics Data System (ADS)

Gazibegović-Busuladžić, A.; Busuladžić, M.; Hasović, E.; Becker, W.; Milošević, D. B.

2018-04-01

Using the improved molecular strong-field approximation, we investigate (high-order) above-threshold ionization [(H)ATI] of various linear polyatomic molecules by a two-color laser field of frequencies r ω and s ω (with integer numbers r and s ) having coplanar counter-rotating circularly polarized components (a so-called bicircular field). Reflection and rotational symmetries for molecules aligned in the laser-field polarization plane, analyzed for diatomic homonuclear molecules in Phys. Rev. A 95, 033411 (2017), 10.1103/PhysRevA.95.033411, are now considered for diatomic heteronuclear molecules and symmetric and asymmetric linear triatomic molecules. There are additional rotational symmetries for (H)ATI spectra of symmetric linear molecules compared to (H)ATI spectra of the asymmetric ones. It is shown that these symmetries manifest themselves differently for r +s odd and r +s even. For example, HATI spectra for symmetric molecules with r +s even obey inversion symmetry. For ATI spectra of linear molecules, reflection symmetry appears only for certain molecular orientation angles ±90∘-j r 180∘/(r +s ) (j integer). For symmetric linear molecules, reflection symmetry appears also for the angles -j r 180∘/(r +s ) . For perpendicular orientation of molecules with respect to the laser-field polarization plane, the HATI spectra are very similar to those of the atomic targets, i.e., both spectra are characterized by the same type of the (r +s )-fold symmetry.

On the dynamics of chain systems. [applications in manipulator and human body models

NASA Technical Reports Server (NTRS)

Huston, R. L.; Passerello, C. E.

1974-01-01

A computer-oriented method for obtaining dynamical equations of motion for chain systems is presented. A chain system is defined as an arbitrarily assembled set of rigid bodies such that adjoining bodies have at least one common point and such that closed loops are not formed. The equations of motion are developed through the use of Lagrange's form of d'Alembert's principle. The method and procedure is illustrated with an elementary study of a tripod space manipulator. The method is designed for application with systems such as human body models, chains and cables, and dynamic finite-segment models.

Strain and Polarization Studies of InGaN for Optoelectronic, Electronic, and Photovoltaic Applications

DTIC Science & Technology

2009-12-14

10.1 A general QWR within a bimaterial substrate: An eigenstrain γ∗i j is applied to the QWR which is an arbitrarily shaped polygon... eigenstrain [15]. As QWR arrays can be self-organized layer-by- layer and also can be grown in different orientations, a more realistic QWR...is the sum γI j = γeI j + γ ∗ I j (2.3) where γ∗I j is the extended eigenstrain in the QWR, and γeI j the extended strain that appears in the

Crack problems for a rectangular plate and an infinite strip

NASA Technical Reports Server (NTRS)

Civelek, M. B.; Erdogan, F.

1980-01-01

The general plane problem for an infinite strip containing multiple cracks perpendicular to its boundaries is considered. The problem is reduced to a system of singular integral equations. Two specific problems of practical interest are then studied in detail. The first problem explores the interaction effect of multiple edge cracks in a plate or beam under tension or bending. The second problem is that of a rectangular plate containing an arbitrarily oriented crack in the plane of symmetry. Particular emphasis is placed on the problem of a plate containing an edge crack and subjected to concentrated forces.

Effect of Bacterial Microbiota on the Silica Uptake of the Marine Diatom, Odontella sp.

NASA Astrophysics Data System (ADS)

Hughes, E. J.; Kempnich, M.; Sison-Mangus, M.

2016-12-01

Diatoms are the most prolific primary producers in the ocean and are known to dominate the phytoplankton community when nutrients become available. Diatoms require silica for growth in order to produce their silica wall frustules. Studies pertaining to silica uptake in diatoms have recently become possible with the use of PDMPO [2-(4-pyridyl)-5{[4-dimethylaminoethyl-aminocarbamoyl]-methoxy}phenyl]oxazole], a dye which selectively binds to free silica and can effectively be used to demonstrate silica uptake and deposition in diatoms. Many factors affect the growth of diatoms, including their bacterial associates or microbiome. Some members of their microbiota can increase diatom growth while others stunt their growth and eventually lyse them. Bacteria-free diatoms, on the other hand, have significantly lower growth than diatoms associating with bacteria. Here we ask if the silica uptake of Odontella sp. was influenced by co-culture with various types of bacteria. Silicification was measured using spectrophotometry to calculate PDMPO concentration as a proxy for silica uptake. We found that axenic cultures have the lowest silica uptake while non-axenic diatoms and diatoms co-cultured with the bacteria from Bacteroidetes (Cellulophaga), Firmicutes (Planococcus) and Gamma-proteobacteria (Vibrio) have varying effects on the silica uptake of the 3 diatoms. This study adds another piece of evidence that bacteria can play an important role on the growth and development of the diatoms. This work suggests that different types of bacteria can have a profound effect on the survival and ecological success of diatoms and bacterial associates should be considered when studying diatom's biology and ecology.

[Research advances in heavy metals pollution ecology of diatom].

PubMed

Ding, Teng-Da; Ni, Wan-Min; Zhang, Jian-Ying

2012-03-01

Diatom, due to its high sensitivity to environmental change, is one of the bio-indicators of aquatic ecosystem health, and some typical diatom species have been applied to indicate the heavy metals pollution of water body. With the focus on the surface water heavy metals pollution, this paper reviewed the research advances in the toxic effect of heavy metals pollution on diatom, biosorption and bioaccumulation of heavy metals by diatom, ecological adaptation mechanisms of diatom to heavy metals pollution, and roles of diatom as bio-indicator and in ecological restoration of heavy metals pollution. The growth tendency of diatom and the morphological change of frustule under heavy metals pollution as well as the differences in heavy metals biosorption and bioaccumulation by diatom, the ecological adaptation mechanisms of diatom on heavy metals surface complexation and ion exchange, and the roles of diatom as bio-indicator and in ecological restoration of heavy metals polluted water body were also discussed. This review could provide scientific evidences for the prevention of aquatic ecosystems heavy metals pollution and related early warning techniques.

Fossil diatoms and neogene paleolimnology

USGS Publications Warehouse

Platt, Bradbury J.

1988-01-01

Diatoms have played an important role in the development of Neogene continental biostratigraphy and paleolimnology since the mid-19th Century. The history of progress in Quaternary diatom biostratigraphy has developed as a result of improved coring techniques that enable sampling sediments beneath existing lakes coupled with improved chronological control (including radiometric dating and varve enumeration), improved statistical treatment of fossil diatom assemblages (from qualitative description to influx calculations of diatom numbers or volumes), and improved ecological information about analogous living diatom associations. The last factor, diatom ecology, is the most critical in many ways, but progresses slowly. Fortunately, statistical comparison of modern diatom assemblages and insightful studies of the nutrient requirements of some common freshwater species are enabling diatom paleolimnologists to make more detailed interpretations of the Quaternary record than had been possible earlier, and progress in the field of diatom biology and ecology will continue to refine paleolimnological studies. The greater age and geologic setting of Tertiary diatomaceous deposits has prompted their study in the contexts of geologic history, biochronology and evolution. The distribution of diatoms of marine affinities in continental deposits has given geologists insights about tectonism and sea-level change, and the distribution of distinctive (extinct?) diatoms has found utilization both in making stratigraphic correlations between outcrops of diatomaceous deposits and in various types of biochronological studies that involve dating deposits in different areas. A continental diatom biochronologic scheme will rely upon evolution, such as the appearance of new genera within a family, in combination with regional environmental changes that are responsible for the wide distribution of distinctive diatom species. The increased use of the scanning electron microscope for the detailed descriptions of fossil diatoms will provide the basis for making more accurate correlations and identifications, and the micromorphological detail for speculations about evolutionary relationships. ?? 1988.

Prevalence of diatom frustules in non-vegetarian foodstuffs and its implications in interpreting identification of diatom frustules in drowning cases.

PubMed

Yen, Law Yen; Jayaprakash, P T

2007-07-20

Detection of diatom frustules in bone marrow (diatom test) is used for diagnosing ante-mortem drowning where the usual signs of drowning are not present in dead bodies recovered from water. However, controversies over the reliability of diatom test results are continuing. There have been indications on the possibilities of diatoms entering into systemic circulation from atmospheric air, food and drink. While diatoms have been demonstrated in the gut content of edible marine forms such as shrimps and clams, the present study, for the first time, provides empirical evidence on the prevalence as well as abundance of diatom frustules in the samples of cooked non-vegetarian foodstuffs that impend human consumption in Kelantan, Malaysia. It is found that 50 g each of cleaned and cooked prawns and of clams impending human consumption contain about 8360 and 29,054 diatom frustules, respectively. A person accustomed to prawn and clam food would be ingesting an estimated 2 million diatoms in a single year. Considering the suggestion that detection of five diatom frustules in 10 g of bone marrow would suffice for concluding drowning as mode of death, and the fact that there is yet no proof that diatom frustules do not enter into the human systemic circulation through the digestive tract, the estimated number of diatom frustules routinely ingested acquires significance since entry of a few of such ingested frustules into the systemic circulation can lead to false positive test results. The findings of this research raise two important issues: first, population based routine food related diatom ingestion requires to be estimated, and, second, studies have to be initiated to categorically prove or disprove the possibility of entry of diatom frustules into the systemic circulation via the digestive tract.

Diatom diet selectivity by early post-larval abalone Haliotis diversicolor supertexta under hatchery conditions

NASA Astrophysics Data System (ADS)

Zhang, Yuyu; Gao, Yahui; Liang, Junrong; Chen, Changping; Zhao, Donghai; Li, Xuesong; Li, Yang; Wu, Wenzhong

2010-11-01

Benthic diatoms constitute the primary diet of abalone during their early stages of development. To evaluate the dietary preferences of early post-larval abalone, Haliotis diversicolor supertexta, we analyzed the gut contents of post-larvae that settled on diatom films. We compared the abundance and species diversity of diatom assemblages in the gut to those of the epiphytic diatom assemblages on the attachment films, and identified 40 benthic diatom species in the gut contents of post-larvae 12 to 24 d after settlement. The most abundant taxa in the gut contents were Navicula spp., Amphora copulate, and Amphora coffeaeformis. Navicula spp. accounted for 64.0% of the cell density. In the attachment films, we identified 110 diatom species belonging to 38 genera. Pennate diatoms were the dominant members including the species Amphiprora alata, Cocconeis placentula var. euglypta, Cylindrotheca closterium, Navicula sp. 2, and A. coffeaeformis. Nano-diatoms (<20 μm in length) accounted for a considerable proportion of the total species number and cell density of the diatom assemblages in the gut contents and on the films. This suggests that nano-diatoms are important to the efficient production of abalone seed. The difference of the composition and abundance of diatoms between in the guts and on the biofilms suggests that early post-larval grazing was selective. An early post-larval abalone preferred nano-diatoms and the genera Navicula and Amphora during the month after settlement.

Rabi oscillations in the dissociative continuum: Rotation and alignment effects

NASA Astrophysics Data System (ADS)

Granucci, Giovanni; Magnier, Sylvie; Persico, Maurizio

2002-01-01

We have simulated a set of experiments in which Rabi oscillations are induced in bound-free and free-free transitions of a diatomic molecule. Dissociative vibrational states belonging to different electronic terms are involved. We show analytically and confirm computationally that a simple relationship exists between the one-dimensional dynamics of a molecule with fixed orientation with respect to the polarization of the radiation field and the three-dimensional dynamics of a rotating system. It is demonstrated that sufficiently short laser pulses can induce oscillations in the probabilities of two coupled electronic states, and in the yields of the respective dissociation products, as functions of the radiation intensity. As a result of molecular rotation the oscillations are damped but not washed out. The initial thermal distribution on several rotational levels has a negligible effect on the photodissociation yields and other experimentally relevant quantities. Since the molecule undergoes a strong alignment along the polarization axis of the laser field, the ejection of atoms and ions is anisotropic. We have chosen the well known diatomic ion Na2+ as a convenient example.

Theory of diatomic molecules in an external electromagnetic field from first quantum mechanical principles.

PubMed

Sindelka, Milan; Moiseyev, Nimrod

2006-04-27

We study a general problem of the translational/rotational/vibrational/electronic dynamics of a diatomic molecule exposed to an interaction with an arbitrary external electromagnetic field. The theory developed in this paper is relevant to a variety of specific applications, such as alignment or orientation of molecules by lasers, trapping of ultracold molecules in optical traps, molecular optics and interferometry, rovibrational spectroscopy of molecules in the presence of intense laser light, or generation of high order harmonics from molecules. Starting from the first quantum mechanical principles, we derive an appropriate molecular Hamiltonian suitable for description of the center of mass, rotational, vibrational, and electronic molecular motions driven by the field within the electric dipole approximation. Consequently, the concept of the Born-Oppenheimer separation between the electronic and the nuclear degrees of freedom in the presence of an electromagnetic field is introduced. Special cases of the dc/ac-field limits are then discussed separately. Finally, we consider a perturbative regime of a weak dc/ac field, and obtain simple analytic formulas for the associated Born-Oppenheimer translational/rotational/vibrational molecular Hamiltonian.

Doping of magnetite nanoparticles facilitates clean harvesting of diatom oil as biofuel for sustainable energy

NASA Astrophysics Data System (ADS)

Kumar, Vikas; Singh, Ramesh; Thakur, Shipra; Ballabh Joshi, Khashti; Vinayak, Vandana

2018-04-01

Photosynthetic unicellular brown algae diatoms are considered as photobioreactors (PBRs) that synthesize and store oil in the form of lipid droplets and the much of the crude oil we use comes from fossil diatoms. The clean extraction of this crude oil from diatoms is difficult task. The construction of green chemical protocols for the clean separation of diatom oil from cells without killing or to harm the diatom cells is still in its primitive stage. In this report we would like to propose that facile doping of magnetite on diatoms can be used for clean oil separation in PBRs. We doped magnetite nanoparticles onto the surface of diatom Diadesmis confervaceae a diatom which oozes oil naturally. Doping magnetite onto diatoms can also facilitate easy separation of oil when cells are kept in an electromagnetic field. The cell wall of diatom besides having SiOH group has 281 amino acids of which 187–188 amino acids are conserved and are known for metal binding sites. The magnetite nanoparticles bind to the SiOH groups and metal binding sites of amino acids. The presence of appropriate amine functionalized linkers forming peptide aminosilane shells can further facilitate the binding of peptide/polypeptides which can be used in drug delivery. Besides this the magnetite doped diatoms have wide applications in removal of phosphates and chromium from waste water too.

Analysis of change of red tide species in Yodo River estuary by the numerical ecosystem model.

PubMed

Hayashi, Mitsuru; Yanagi, Tetsuo

2008-01-01

Occurrence number of red tides in Osaka Bay in Japan is more than 20 cases every year. Diatom red tide was dominant in Osaka Bay, but the non-diatom red tide was dominant in early 1990s. Therefore, the material cycling in Yodo River estuary in Osaka Bay during August from 1991 to 2000 was analyzed by using the numerical ecosystem model and field observation data to clarify the reasons of change in red tide species. Year-to-year variation in calculated concentration ratio of diatom to non-diatom corresponds to the variation in observed ratio of red tide days of diatom to non-diatom. Limiting nutrient of primary production is phosphate over the period. Diatom dominated from 1991 to 1993, but it was difficult for non-diatom to grow due to the limitation by physical condition. Non-diatom was able to grow because of good physical and nutrient conditions from 1994 to 1996. And diatom dominated again under the good physical condition, and phosphorus supply was not enough for non-diatom to grow from 1998 to 2000. Phosphate concentration in the lower layer of Yodo River estuary was important to the variation in red tide species in the upper layer of Yodo River estuary.

Comprehensive Fe-ligand vibration identification in {FeNO} 6 Hemes

DOE PAGES

Li, Jianfeng; Peng, Qian; Oliver, Allen G.; ...

2014-12-09

Oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) has been used to obtain all iron vibrations in two {FeNO} 6 porphyrinate complexes, five-coordinate [Fe(OEP)(NO)]ClO 4 and six-coordinate [Fe(OEP)(2-MeHIm)(NO)]ClO 4. A new crystal structure was required for measurements of [Fe(OEP)(2-MeHIm)(NO)]ClO 4, and the new structure is reported herein. Single crystals of both complexes were oriented to be either parallel or perpendicular to the porphyrin plane and/or axial imidazole ligand plane. Thus, the FeNO bending and stretching modes can now be unambiguously assigned; the pattern of shifts in frequency as a function of coordination number can also be determined. The pattern is quitemore » distinct from those found for CO or {FeNO} 7 heme species. This is the result of unchanging Fe–N NO bonding interactions in the {FeNO} 6 species, in distinct contrast to the other diatomic ligand species. DFT calculations were also used to obtain detailed predictions of vibrational modes. Predictions were consistent with the intensity and character found in the experimental spectra. The NRVS data allow the assignment and observation of the challenging to obtain Fe–Im stretch in six-coordinate heme derivatives. Furthermore, NRVS data for this and related six-coordinate hemes with the diatomic ligands CO, NO, and O 2 reveal a strong correlation between the Fe–Im stretch and Fe–N Im bond distance that is detailed for the first time.« less

Diatom-Specific Oligosaccharide and Polysaccharide Structures Help to Unravel Biosynthetic Capabilities in Diatoms.

PubMed

Gügi, Bruno; Le Costaouec, Tinaïg; Burel, Carole; Lerouge, Patrice; Helbert, William; Bardor, Muriel

2015-09-18

Diatoms are marine organisms that represent one of the most important sources of biomass in the ocean, accounting for about 40% of marine primary production, and in the biosphere, contributing up to 20% of global CO₂ fixation. There has been a recent surge in developing the use of diatoms as a source of bioactive compounds in the food and cosmetic industries. In addition, the potential of diatoms such as Phaeodactylum tricornutum as cell factories for the production of biopharmaceuticals is currently under evaluation. These biotechnological applications require a comprehensive understanding of the sugar biosynthesis pathways that operate in diatoms. Here, we review diatom glycan and polysaccharide structures, thus revealing their sugar biosynthesis capabilities.

Point force and point electric charge applied to the boundary of three-dimensional anisotropic piezoelectric solid

DOE PAGES

Borovikov, V. A.; Kalinin, S. V.; Khavin, Yu.; ...

2015-08-19

We derive the Green's functions for a three-dimensional semi-infinite fully anisotropic piezoelectric material using the plane wave theory method. The solution gives the complete set of electromechanical fields due to an arbitrarily oriented point force and a point electric charge applied to the boundary of the half-space. Moreover, the solution constitutes generalization of Boussinesq's and Cerruti's problems of elastic isotropy for the anisotropic piezoelectric materials. On the example of piezoceramics PZT-6B, the present results are compared with the previously obtained solution for the special case of transversely isotropic piezoelectric solid subjected to the same boundary condition.

An elastic strip with multiple cracks and applications to tapered specimens

NASA Technical Reports Server (NTRS)

Liu, X.-H.; Erdogan, F.

1985-01-01

In this paper an infinite elastic strip containing arbitrarily oriented cracks and subjected to uniform tension and a pair of concentrated forces is formulated in terms of a system of singular integral equations. Even though the technique is sufficiently general to solve new multiple crack problem, with the objective of applying the results to tapered specimens, only a certain symmetric crack geometry and loading conditions are considered. The stress intensity factors are calculated for edge cracks in the strip under uniform tension and for a 'compact' and a 'slender' tapered specimen (the latter simulating the double cantilever beam) under concentrated forces or crack surface wedge forces.

Plasma expansion into a vacuum with an arbitrarily oriented external magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

García-Rubio, F., E-mail: fernando.garcia.rubio@upm.es; Sanz, J.; Ruocco, A.

2016-01-15

Plasma expansion into a vacuum with an external magnetic field is studied under the ideal magnetohydrodynamic hypothesis. The inclination of the magnetic field with respect to the expansion direction is arbitrary, and both the perpendicular and the oblique cases are separately analyzed. A self-similar solution satisfying the boundary conditions is obtained. The interface with the vacuum is treated as a fluid surface, and jump conditions concerning the momentum conservation are imposed. The effect of the intensity of the magnetic field and its inclination is thoroughly studied, and the consistency of the solution for small and large inclinations is investigated.

Environmental investigations using diatom microfossils

USGS Publications Warehouse

Smith, Kathryn E.L.; Flocks, James G.

2010-01-01

Diatoms are unicellular phytoplankton (microscopic plant-like organisms) with cell walls made of silica (called a frustule). They live in both freshwater and saltwater and can be found in just about every place on Earth that is wet. The shape and morphology of the diatom frustule unique to each species are used for identification. Due to the microscopic size of diatoms, high-power microscopy is required for diatom identification. Diatoms are vital to life on Earth. They are photosynthetic primary producers, using sunlight to create oxygen and organic carbon from carbon dioxide and water. They are a significant source of the oxygen we breathe, have a major impact on the global carbon cycle (Smetacek, 1999), and are a food source for many aquatic organisms (Mann, 1993). Diatom abundance has even been demonstrated to have an influence on the diversity of larger marine mammals, including whales (Marx and Uhen, 2010). Data on diatom abundance and diversity are extremely useful in environmental studies.

Diatom-Specific Oligosaccharide and Polysaccharide Structures Help to Unravel Biosynthetic Capabilities in Diatoms

PubMed Central

Gügi, Bruno; Le Costaouec, Tinaïg; Burel, Carole; Lerouge, Patrice; Helbert, William; Bardor, Muriel

2015-01-01

Diatoms are marine organisms that represent one of the most important sources of biomass in the ocean, accounting for about 40% of marine primary production, and in the biosphere, contributing up to 20% of global CO2 fixation. There has been a recent surge in developing the use of diatoms as a source of bioactive compounds in the food and cosmetic industries. In addition, the potential of diatoms such as Phaeodactylum tricornutum as cell factories for the production of biopharmaceuticals is currently under evaluation. These biotechnological applications require a comprehensive understanding of the sugar biosynthesis pathways that operate in diatoms. Here, we review diatom glycan and polysaccharide structures, thus revealing their sugar biosynthesis capabilities. PMID:26393622

Inspiring the Next Generation of Scientists: Building on 52 Years of Tradition in Diatom Research with Open-Source, Web-Based Collaboration Tools and Online Resources in a Field Course for High School Students

NASA Astrophysics Data System (ADS)

Howard, K. L.; Lee, S. S.

2015-12-01

Open-source, web-based forums and online resources can be used to develop a collaborative, active-learning approach for engaging and training students in the scientific process. We used the Diatoms of the United States website as an online resource for diatom taxonomy and developed a Google+ class community to serve as a platform for high school students to learn about research in diatom taxonomy, community ecology and diatom applications to the earth sciences. Ecology and Systematics of Diatoms is a field course that has been taught at the undergraduate and graduate levels at the Iowa Lakeside Lab field station for 52 years, beginning with the Diatom Clinic in 1963. Freshwater diatom education at Lakeside Lab has since evolved into a foundational training course attracting budding diatomists from all over the world, and has grown to include a week-long course for high school students. Successful since 2012, the high school course is now offered for college credit (University of Iowa), and covers methods of diatom specimen collection and preparation, microscopy, identification of diatom genera, diatom ecology, applications of diatom research, and an introduction to data analysis incorporating multivariate statistics (ordination) using the R statistical program, as well as primary scientific literature. During the 2015 course, students contributed to a Google+ class community where they posted images, data, and questions. The web-based platform allowed students to easily share information and to give and receive feedback from both peers and instructors. Students collaborated via the Google+ community and used the Diatoms of the United States website to develop a taxonomic reference for a field-based group research project, simulating how an actual diatom research program would develop a region or project-specific flora harmonized across analysts. Students investigated the taxonomy and ecology of diatom epiphytes on the green alga Cladophora from the littoral zone of West Lake Okoboji, Iowa. They found the epiphyte community went through a seasonal succession and developed hypotheses for the observed patterns by researching the ecology of diatoms in primary literature. These course activities may be used as a model for other field-based courses or educational programs in earth and environmental sciences.

Seasonal variations in fouling diatom communities on the Yantai coast

NASA Astrophysics Data System (ADS)

Yang, Cuiyun; Wang, Jianhua; Yu, Yang; Liu, Sujing; Xia, Chuanhai

2015-03-01

Fouling diatoms are a main component of biofilm, and play an important role in marine biofouling formation. We investigated seasonal variations in fouling diatom communities that developed on glass slides immersed in seawater, on the Yantai coast, northern Yellow Sea, China, using microscopy and molecular techniques. Studies were conducted during 2012 and 2013 over 3, 7, 14, and 21 days in each season. The abundance of attached diatoms and extracellular polymeric substances increased with exposure time of the slides to seawater. The lowest diatom density appeared in winter and the highest species richness and diversity were found in summer and autumn. Seasonal variation was observed in the structure of fouling diatom communities. Pennate diatoms Cylindrotheca, Nitzschia, Navicula, Amphora, Gomphonema, and Licmophora were the main fouling groups. Cylindrotheca sp. dominated in the spring. Under laboratory culture conditions, we found that Cylindrotheca grew very fast, which might account for the highest density of this diatom in spring. The lower densities in summer and autumn might result from the emergence of fouling animals and environmental factors. The Cylindrotheca sp. was identified as Cylindrotheca closterium using18S rDNA sequencing. The colonization process of fouling diatoms and significant seasonal variation in this study depended on environmental and biological factors. Understanding the basis of fouling diatoms is essential and important for developing new antifouling techniques.

Shared Epizoic Taxa and Differences in Diatom Community Structure Between Green Turtles (Chelonia mydas) from Distant Habitats.

PubMed

Majewska, Roksana; de Vijver, Bart Van; Nasrolahi, Ali; Ehsanpour, Maryam; Afkhami, Majid; Bolaños, Federico; Iamunno, Franco; Santoro, Mario; De Stefano, Mario

2017-11-01

The first reports of diatoms growing on marine mammals date back to the early 1900s. However, only recently has direct evidence been provided for similar associations between diatoms and sea turtles. We present a comparison of diatom communities inhabiting carapaces of green turtles Chelonia mydas sampled at two remote sites located within the Indian (Iran) and Atlantic (Costa Rica) Ocean basins. Diatom observations and counts were carried out using scanning electron microscopy. Techniques involving critical point drying enabled observations of diatoms and other microepibionts still attached to sea turtle carapace and revealed specific aspects of the epizoic community structure. Species-poor, well-developed diatom communities were found on all examined sea turtles. Significant differences between the two host sea turtle populations were observed in terms of diatom abundance and their community structure (including growth form structure). A total of 12 and 22 diatom taxa were found from sea turtles in Iran and Costa Rica, respectively, and eight of these species belonging to Amphora, Chelonicola, Cocconeis, Navicula, Nitzschia and Poulinea genera were observed in samples from both locations. Potential mechanisms of diatom dispersal and the influence of the external environment, sea turtle behaviour, its life stage, and foraging and breeding habitats, as well as epibiotic bacterial flora on epizoic communities, are discussed.

Effects of growth and dissolution on the fractionation of silicon isotopes by estuarine diatoms

NASA Astrophysics Data System (ADS)

Sun, Xiaole; Olofsson, Martin; Andersson, Per S.; Fry, Brian; Legrand, Catherine; Humborg, Christoph; Mörth, Carl-Magnus

2014-04-01

Studies of silicon (Si) isotope fractionation during diatom growth in open ocean systems have documented lower Si isotopic values (δ30Si) in the biogenic silica of diatom frustules compared to dissolved silicon. Recent findings also indicate that Si isotope fractionation occurs during dissolution of diatom frustules, producing higher δ30Si values in the remaining biogenic silica. This study focuses on diatoms from high production areas in estuarine and coastal areas that represent approximately 30-50% of the global marine primary production. Two species of diatoms, Thalassiosira baltica and Skeletonema marinoi, were isolated from the brackish Baltic Sea, one of the largest estuarine systems in the world. These species were used for laboratory investigations of Si isotope fractionation during diatom growth and the subsequent dissolution of the diatom frustules. Both species of diatoms give an identical Si isotope fractionation factor during growth of -1.50 ± 0.36‰ (2σ) for 30Si, which falls in the range of -2.09‰ to -0.55‰ of published data. Our results also suggest a dissolution-induced Si isotope fractionation factor of -0.86‰ at early stage of dissolution, but this effect was observed only in DSi and no significant Si isotope change was observed for BSi. The growth and dissolution results are applied to a Baltic Sea sediment core to reconstruct DSi utilization by diatoms, and found to be in agreement with the observed DSi uptake rates in the overlying water column during diatom growth.

Using benthic diatom assemblages to assess human impacts on streams across a rural to urban gradient.

PubMed

Yang, Ying; Cao, Jin-Xiang; Pei, Guo-Feng; Liu, Guo-Xing

2015-11-01

Benthic diatom assemblages on the natural substrata were investigated at 21 sites of the Ganhe River watershed (China) once per season and in addition, early spring in 2013. A total of 487 diatom taxa from 36 genera were identified during five investigations. The assemblages were dominated by Achnanthidium minutissimum (Kützing) Czarnecki and Cocconeis placentula in the rural reach, whereas Navicula, Nitzschia, and Gomphonema species were characteristic of urbanized sites. Our results suggest that biodiversity was positively related to high nutrient levels and strongly negatively related to diatom-based indices. The periphyton biomass (expressed as chlorophyll a and ash-free dry mass) was not related to water quality. Canonical correspondence analysis (CCA) showed that the nutrient concentration gradient was the most important factor that affected the diatom assemblage composition and species distribution. The diatom-based indices (specific pollution sensitivity index (IPS), biological diatom index (IBD), and trophic diatom index (TDI)) were significantly positively correlated with water quality and are adequate for use in China. Slight changes in the biodiversity and diatom-based indices followed a temporal pattern. The species composition was less related to the season or hydrological characteristics of the river but more strongly related to differences in the trophic status. In this region, urbanization masked the impact of rural land use on benthic diatoms. The research will expand the understanding of using benthic diatom assemblages for water quality monitoring in urban streams and improve watershed-scale management and conservation efforts in the Ganhe River, China.

Diatom species abundance and morphologically-based dissolution proxies in coastal Southern Ocean assemblages

NASA Astrophysics Data System (ADS)

Warnock, Jonathan P.; Scherer, Reed P.

2015-07-01

Taphonomic processes alter diatom assemblages in sediments, thus potentially negatively impacting paleoclimate records at various rates across space, time, and taxa. However, quantitative taphonomic data is rarely included in diatom-based paleoenvironmental reconstructions and no objective standard exists for comparing diatom dissolution in sediments recovered from marine depositional settings, including the Southern Ocean's opal belt. Furthermore, identifying changes to diatom dissolution through time can provide insight into the efficiency of both upper water column nutrient recycling and the biological pump. This is significant in that reactive metal proxies (e.g. Al, Ti) in the sediments only account for post-depositional dissolution, not the water column where the majority of dissolution occurs. In order to assess the range of variability of responses to dissolution in a typical Southern Ocean diatom community and provide a quantitative guideline for assessing taphonomic variability in diatoms recovered from core material, a sediment trap sample was subjected to controlled, serial dissolution. By evaluating dissolution-induced changes to diatom species' relative abundance, three preservational categories of diatoms have been identified: gracile, intermediate, and robust. The relative abundances of these categories can be used to establish a preservation grade for diatom assemblages. However, changes to the relative abundances of diatom species in sediment samples may reflect taphonomic or ecological factors. In order to address this complication, relative abundance changes have been tied to dissolution-induced morphological change to the areolae of Fragilariopsis curta, a significant sea-ice indicator in Southern Ocean sediments. This correlation allows differentiation between gracile species loss to dissolution versus ecological factors or sediment winnowing. These results mirror a similar morphological dissolution index from a parallel study utilizing Fragilariopsis kerguelensis, suggesting that results are applicable to a broad spectrum of diatoms typically preserved in the sediments.

Automated Diatom Analysis Applied to Traditional Light Microscopy: A Proof-of-Concept Study

NASA Astrophysics Data System (ADS)

Little, Z. H. L.; Bishop, I.; Spaulding, S. A.; Nelson, H.; Mahoney, C.

2017-12-01

Diatom identification and enumeration by high resolution light microscopy is required for many areas of research and water quality assessment. Such analyses, however, are both expertise and labor-intensive. These challenges motivate the need for an automated process to efficiently and accurately identify and enumerate diatoms. Improvements in particle analysis software have increased the likelihood that diatom enumeration can be automated. VisualSpreadsheet software provides a possible solution for automated particle analysis of high-resolution light microscope diatom images. We applied the software, independent of its complementary FlowCam hardware, to automated analysis of light microscope images containing diatoms. Through numerous trials, we arrived at threshold settings to correctly segment 67% of the total possible diatom valves and fragments from broad fields of view. (183 light microscope images were examined containing 255 diatom particles. Of the 255 diatom particles present, 216 diatoms valves and fragments of valves were processed, with 170 properly analyzed and focused upon by the software). Manual analysis of the images yielded 255 particles in 400 seconds, whereas the software yielded a total of 216 particles in 68 seconds, thus highlighting that the software has an approximate five-fold efficiency advantage in particle analysis time. As in past efforts, incomplete or incorrect recognition was found for images with multiple valves in contact or valves with little contrast. The software has potential to be an effective tool in assisting taxonomists with diatom enumeration by completing a large portion of analyses. Benefits and limitations of the approach are presented to allow for development of future work in image analysis and automated enumeration of traditional light microscope images containing diatoms.

Auxosporulation in Paralia guyana MacGillivary (Bacillariophyta) and Possible New Insights into the Habit of the Earliest Diatoms

PubMed Central

Kaczmarska, Irena; Ehrman, James M.

2015-01-01

Background Diatoms are one of the most ecologically important aquatic micro-eukaryotes. As a group unambiguously recognized as diatoms, they seem to have appeared relatively recently with a limited record of putative remains from oldest sediments. In contrast, molecular clock estimates for the earliest possible emergence of diatoms suggest a considerably older date. Depending on the analysis, Paralia and Leptocylindrus have been recovered within the basal molecular divergences of diatoms. Thus these genera may be in the position to inform on characters that the earliest diatoms possessed. Findings Here we present auxospore development and structure of initial and post-auxospore cells in a representative of the ancient non-polar centric genus Paralia. Their initial frustules showed unusual, but not unprecedented, spore-like morphology. Similarly, initial frustules of Leptocylindrus have been long considered resting spores and a unique peculiarity of this genus. However, even though spore-like in appearance, initial cells of Paralia readily resumed mitotic divisions. In addition, Paralia post-auxospore cells underwent several rounds of mitoses in a multi-step process of building a typical, “perfect” vegetative valve. This degree of heteromorphy immediately post-auxosporulation is thus far unknown among the diatoms. Implications A spore-related origin of diatoms has already been considered, most recently in the form of the “multiplate diploid cyst” hypothesis. Our discovery that the initial cells in some of the most ancient diatom lineages are structurally spore-like is consistent with that hypothesis because the earliest diatoms may be expected to look somewhat similar to their ancestors. We speculate that because the earliest diatoms may have appeared less diatom-like and more spore-like, they could have gone unrecognized as such in the Triassic/Jurassic sediments. If correct, diatoms may indeed be much older than the fossil record indicates, and possibly more in line with some molecular clock predictions. PMID:26485144

Interactive effects of and light on growth rates and RUBISCO content of small and large centric diatoms

NASA Astrophysics Data System (ADS)

Li, G.; Campbell, D. A.

2015-10-01

Among marine phytoplankton groups, diatoms span the widest range of cell size, with resulting effects upon their nitrogen uptake, photosynthesis and growth responses to light. We grew two strains of marine centric diatoms, the small Thalassiosira pseudonana and the larger T. punctigera in high and low nitrogen media, across a range of growth light levels. Nitrogen and total proteins per cell decreased with increasing growth light in both species when grown under low nitrogen media. Surprisingly, low nitrogen increased the cellular allocation to RUBISCO and the rate of electron transport away from Photosystem II for the smaller diatom under low growth light, and for the larger diatom across the range of growth lights. Low nitrogen decreased the growth rate of the smaller diatom, particularly under higher light, but stimulated the growth rate of the larger diatom. Our results show that the high nitrogen in common growth media favours the growth rate of a small diatom but inhibits growth of a larger species.

Microbial control of diatom bloom dynamics in the open ocean

NASA Astrophysics Data System (ADS)

Boyd, Philip W.; Strzepek, Robert; Chiswell, Steve; Chang, Hoe; DeBruyn, Jennifer M.; Ellwood, Michael; Keenan, Sean; King, Andrew L.; Maas, Elisabeth W.; Nodder, Scott; Sander, Sylvia G.; Sutton, Philip; Twining, Benjamin S.; Wilhelm, Steven W.; Hutchins, David A.

2012-09-01

Diatom blooms play a central role in supporting foodwebs and sequestering biogenic carbon to depth. Oceanic conditions set bloom initiation, whereas both environmental and ecological factors determine bloom magnitude and longevity. Our study reveals another fundamental determinant of bloom dynamics. A diatom spring bloom in offshore New Zealand waters was likely terminated by iron limitation, even though diatoms consumed <1/3 of the mixed-layer dissolved iron inventory. Thus, bloom duration and magnitude were primarily set by competition for dissolved iron between microbes and small phytoplankton versus diatoms. Significantly, such a microbial mode of control probably relies both upon out-competing diatoms for iron (i.e., K-strategy), and having high iron requirements (i.e., r-strategy). Such resource competition for iron has implications for carbon biogeochemistry, as, blooming diatoms fixed three-fold more carbon per unit iron than resident non-blooming microbes. Microbial sequestration of iron has major ramifications for determining the biogeochemical imprint of oceanic diatom blooms.

Self-assembled diatom substrates with plasmonic functionality

NASA Astrophysics Data System (ADS)

Kwon, Sun Yong; Park, Sehyun; Nichols, William T.

2014-04-01

Marine diatoms have an exquisitely complex exoskeleton that is promising for engineered surfaces such as sensors and catalysts. For such applications, creating uniform arrays of diatom frustules across centimeter scales will be necessary. Here, we present a simple, low-cost floating interface technique to self-assemble the diatom frustules. We show that well-prepared diatoms form floating hexagonal close-packed arrays at the air-water interface that can be transferred directly to a substrate. We functionalize the assembled diatom surfaces with gold and characterize the plasmonic functionality by using surface enhanced Raman scattering (SERS). Thin gold films conform to the complex, hierarchical diatom structure and produce a SERS enhancement factor of 2 × 104. Small gold nanoparticles attached to the diatom's surface produce a higher enhancement of 7 × 104 due to stronger localization of the surface plasmons. Taken together, the large-scale assembly and plasmonic functionalization represent a promising platform to control the energy and the material flows at a complex surface for applications such as sensors and plasmonic enhanced catalysts.

Analysis of quasi-periodic pore-network structure of centric marine diatom frustules

NASA Astrophysics Data System (ADS)

Cohoon, Gregory A.; Alvarez, Christine E.; Meyers, Keith; Deheyn, Dimitri D.; Hildebrand, Mark; Kieu, Khanh; Norwood, Robert A.

2015-03-01

Diatoms are a common type of phytoplankton characterized by their silica exoskeleton known as a frustule. The diatom frustule is composed of two valves and a series of connecting girdle bands. Each diatom species has a unique frustule shape and valves in particular species display an intricate pattern of pores resembling a photonic crystal structure. We used several numerical techniques to analyze the periodic and quasi-periodic valve pore-network structure in diatoms of the Coscinodiscophyceae order. We quantitatively identify defect locations and pore spacing in the valve and use this information to better understand the optical and biological properties of the diatom.

Biomimetic Photonic Crystals based on Diatom Algae Frustules

NASA Astrophysics Data System (ADS)

Mishler, Jonathan; Alverson, Andrew; Herzog, Joseph

2015-03-01

Diatom algae are unicellular, photosynthetic microorganisms with a unique external shell known as a frustule. Frustules, which are composed of amorphous silica, exhibit a unique periodic nano-patterning, distinguishing diatoms from other types of phytoplankton. Diatoms have been studied for their distinctive optical properties due to their resemblance of photonic crystals. In this regard, diatoms are not only considered for their applications as photonic crystals, but also for their use as biomimetic templates for artificially fabricated photonic crystals. Through the examination and measurement of the physical characteristics of many scanning electron microscope (SEM) images of diatom frustules, a biomimetic photonic crystal derived from diatom frustules can be recreated and modeled with the finite element method. In this approach, the average geometries of the diatom frustules are used to recreate a 2-dimensional photonic crystal, after which the electric field distribution and optical transmission through the photonic crystal are both measured. The optical transmission is then compared to the transmission spectra of a regular hexagonal photonic crystal, revealing the effects of diatom geometry on their optical properties. Finally, the dimensions of the photonic crystal are parametrically swept, allowing for further control over the transmission of light through the photonic crystal.

(Bio)Chemical Tailoring of Biogenic 3-D Nanopatterned Templates with Energy-Relevant Functionalities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sandhage, Kenneth H; Kroger, Nils

2014-09-08

The overall aim of this research has been to obtain fundamental understanding of (bio)chemical methodologies that will enable utilization of the unique 3-D nanopatterned architectures naturally produced by diatoms for the syntheses of advanced functional materials attractive for applications in energy harvesting/conversion and storage. This research has been conducted in three thrusts: Thrust 1 (In vivo immobilization of proteins in diatom biosilica) is directed towards elucidating the fundamental mechanism(s) underlying the cellular processes of in vivo immobilization of proteins in diatom silica. Thrust 2 (Shape-preserving reactive conversion of diatom biosilica into porous, high-surface area inorganic replicas) is aimed at understandingmore » the fundamental mechanisms of shape preservation and nanostructural evolution associated with the reactive conversion and/or coating-based conversion of diatom biosilica templates into porous inorganic replicas. Thrust 3 (Immobilization of energy-relevant enzymes in diatom biosilica and onto diatom biosilica-derived inorganic replicas) involves use of the results from both Thrust 1 and 2 to develop strategies for in vivo and in vitro immobilization of enzymes in/on diatom biosilica and diatom biosilica-derived inorganic replicas, respectively. This Final Report describes progress achieved in all 3 of these thrusts.« less

The Microscopic World of Diatoms

ERIC Educational Resources Information Center

Sultany, Molly; Bixby, Rebecca

2016-01-01

For students in biology, chemistry, or environmental science, diatoms offer excellent insight into watershed health and human impact on the environment. Diatoms are found globally in virtually every habitat that has sunlight and moisture, including polar seas, tropical streams, and on moist soils and mosses. Studying diatoms as biological…

Inorganic carbon availability in benthic diatom communities: photosynthesis and migration.

PubMed

Marques da Silva, Jorge; Cruz, Sónia; Cartaxana, Paulo

2017-09-05

Diatom-dominated microphytobenthos (MPB) is the main primary producer of many intertidal and shallow subtidal environments, being therefore of critical importance to estuarine and coastal food webs. Owing to tidal cycles, intertidal MPB diatoms are subjected to environmental conditions far more variable than the ones experienced by pelagic diatoms (e.g. light, temperature, salinity, desiccation and nutrient availability). Nevertheless, benthic diatoms evolved adaptation mechanisms to these harsh conditions, including the capacity to move within steep physical and chemical gradients, allowing them to perform photosynthesis efficiently. In this contribution, we will review present knowledge on the effects of dissolved inorganic carbon (DIC) availability on photosynthesis and productivity of diatom-dominated MPB. We present evidence of carbon limitation of photosynthesis in benthic diatom mats and highly productive MPB natural communities. Furthermore, we hypothesize that active vertical migration of epipelic motile diatoms could overcome local depletion of DIC in the photic layer, providing the cells alternately with light and inorganic carbon supply. The few available longer-term experiments on the effects of inorganic carbon enrichment on the productivity of diatom-dominated MPB have yielded inconsistent results. Therefore, further studies are needed to properly assess the response of MPB communities to increased CO 2 and ocean acidification related to climate change.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Fossil diatom assemblages as paleoecological indicators of paleo-water environmental change in the Ulleung Basin, East Sea, Republic of Korea

NASA Astrophysics Data System (ADS)

Yun, Suk Min; Lee, Taehee; Jung, Seung Won; Park, Joon Sang; Lee, Jin Hwan

2017-09-01

The fossil diatom assemblage record from two sediment cores obtained from the Ulleung Basin, East Sea, Republic of Korea, revealed changes in the diatom assemblage zones in PG1 and PD3 core samples. The two sediment cores were δC14 dated and approximately represented the late Pleistocene-Holocene. The analysis of age zones in the PG1 core and PD3 core was assessed based on the frequency of variations, and occurrences of biostratigraphical fossil diatom species. During the Last Glacial Maximum (LGM), the sea level was lower than that at present and the Ulleung Basin became isolated from the Pacific Ocean. As a result, there would have been a limited Tsushima Warm Current (TWC) influence, and salinity would have decreased resulting in increased freshwater and coastal diatoms. The distribution pattern of diatoms presented in the cores was associated with changes in water temperature and salinity and the adding of terrigenous material brought about by the input of freshwater. Changes in the abundance of a tychopelagic diatom, Paralia sulcata, reflected the effect of the water currents. Diatom temperature (Td) values and the ratio of centric/pennate diatoms provided evidence of limited influences of the TWC and freshwater inflow. It is thought that all assemblage zones were influenced by the TWC, which had an important effect on the distribution and composition of fossil diatoms.

Bacterial Associations with Diatoms Influence Host Health in a Xenic Model System

NASA Astrophysics Data System (ADS)

Baker, L.; Kemp, P. F.

2016-02-01

Diatoms are photosynthetic unicellular eukaryotes found ubiquitously in aquatic systems. Microorganisms such as bacteria are frequently found attached to diatoms and may influence the fitness of their host. The most commonly used model organisms in studies of diatom-bacterial associations are Alteromonas and Marinobacter. Some strains of Alteromonas are capable of parasitism, producing chitinases or having algicidal interactions; some strains of Marinobacter are capable of mutualism, providing its host with vital nutrients. In this study, multiple strains of Alteromonas and Marinobacter were isolated from the centric diatom Chaetoceros sp KBDT20. Isolates were added back in varying concentration to cultures of their original xenic diatom host, and to cultures of a smaller, xenic naïve host, Chaetoceros sp. KBDT32. The growth rate of the diatom host was monitored using flow cytometry to assess the impact of the added bacterial isolates on host health. Our results suggest that all strains of Alteromonas tested have an antagonistic relationship with both the original as well as the naïve host while all strains of Marinobacter tested have a synergistic relationship with both diatom cultures. The functional basis for these relationships is being explored by supplementing xenic diatom cultures with materials essential for diatom growth that may be contributed by bacteria, such as B-vitamins and bioavailable trace metals. The colonization rates and competitive interactions between bacteria are investigated through surface colonization studies. The goal of this study is to better inform our understanding of how bacterial associates of diatom populations may contribute to their health, success, or failure in aquatic systems.

Diatoms and Other Epibionts Associated with Olive Ridley (Lepidochelys olivacea) Sea Turtles from the Pacific Coast of Costa Rica

PubMed Central

Majewska, Roksana; Santoro, Mario; Bolaños, Federico; Chaves, Gerardo; De Stefano, Mario

2015-01-01

Although the sea turtles have long been familiar and even iconic to marine biologists, many aspects of their ecology remain unaddressed. The present study is the first of the epizoic diatom community covering the olive ridley turtle’s (Lepidochelys olivacea) carapace and the first describing diatoms living on sea turtles in general, with the primary objective of providing detailed information on turtle epibiotic associations. Samples of turtle carapace including the associated diatom biofilm and epizoic macro-fauna were collected from Ostional beach (9° 59´ 23.7´´ N 85° 41´ 52.6´´ W), Costa Rica, during the arribada event in October 2013. A complex diatom community was present in every sample. In total, 11 macro-faunal and 21 diatom taxa were recorded. Amongst diatoms, the most numerous were erect (Achnanthes spp., Tripterion spp.) and motile (Haslea sp., Navicula spp., Nitzschia spp., Proschkinia sp.) forms, followed by adnate Amphora spp., while the most common macro-faunal species was Stomatolepas elegans (Cirripedia). Diatom densities ranged from 8179 ± 750 to 27685 ± 4885 cells mm-2. Epizoic microalgae were either partly immersed or entirely encapsulated within an exopolymeric coat. The relatively low diatom species number, stable species composition and low inter-sample dissimilarities (14.4% on average) may indicate a mutualistic relationship between the epibiont and the basibiont. Dispersal of sea turtle diatoms is probably highly restricted and similar studies will help to understand both diatom diversity, evolution and biogeography, and sea turtle ecology and foraging strategies. PMID:26083535

In vivo exposure to northern diatoms arrests sea urchin embryonic development.

PubMed

Gudimova, Elena; Eilertsen, Hans C; Jørgensen, Trond Ø; Hansen, Espen

2016-01-01

There are numerous reports indicating that marine diatoms may act harmful to early developmental stages of invertebrates. It is believed that the compounds responsible for these detrimental effects are oxylipins resulting from oxidized polyunsaturated fatty acids, and that they may function as grazing deterrents. Most studies reporting these effects have exposed test organisms to diatom extracts or purified toxins, but data from in vivo exposure to intact diatoms are scarce. We have conducted sea urchin egg incubation and plutei feeding experiments to test if intact diatom cells affected sea urchin embryo development and survival. This was done by exposing the common northern sea urchins Strongylocentrotus droebachiensis and Echinus acutus to northern strains of the diatoms Chaetoceros socialis, Skeletonema marinoi, Chaetoceros furcellatus, Attheya longicornis, Thalassiosira gravida and Porosira glacialis. The intact diatom cell suspensions were found to inhibit sea urchin egg hatching and embryogenesis. S. marinoi was the most potent one as it caused acute mortality in S. droebachiensis eggs after only four hours exposure to high (50 μg/L Chla) diatom concentrations, as well as 24 h exposure to normal (20 μg/L Chla) and high diatom concentrations. The second most potent species was T. gravida that caused acute mortality after 24 h exposure to both diatom concentrations. A. longicornis was the least harmful of the diatom species in terms of embryo development arrestment, and it was the species that was most actively ingested by S. droebachiensis plutei. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

TAS: A Transonic Aircraft/Store flow field prediction code

NASA Technical Reports Server (NTRS)

Thompson, D. S.

1983-01-01

A numerical procedure has been developed that has the capability to predict the transonic flow field around an aircraft with an arbitrarily located, separated store. The TAS code, the product of a joint General Dynamics/NASA ARC/AFWAL research and development program, will serve as the basis for a comprehensive predictive method for aircraft with arbitrary store loadings. This report described the numerical procedures employed to simulate the flow field around a configuration of this type. The validity of TAS code predictions is established by comparison with existing experimental data. In addition, future areas of development of the code are outlined. A brief description of code utilization is also given in the Appendix. The aircraft/store configuration is simulated using a mesh embedding approach. The computational domain is discretized by three meshes: (1) a planform-oriented wing/body fine mesh, (2) a cylindrical store mesh, and (3) a global Cartesian crude mesh. This embedded mesh scheme enables simulation of stores with fins of arbitrary angular orientation.

Cycle/Cocycle Oblique Projections on Oriented Graphs

NASA Astrophysics Data System (ADS)

Polettini, Matteo

2015-01-01

It is well known that the edge vector space of an oriented graph can be decomposed in terms of cycles and cocycles (alias cuts, or bonds), and that a basis for the cycle and the cocycle spaces can be generated by adding and removing edges to an arbitrarily chosen spanning tree. In this paper, we show that the edge vector space can also be decomposed in terms of cycles and the generating edges of cocycles (called cochords), or of cocycles and the generating edges of cycles (called chords). From this observation follows a construction in terms of oblique complementary projection operators. We employ this algebraic construction to prove several properties of unweighted Kirchhoff-Symanzik matrices, encoding the mutual superposition between cycles and cocycles. In particular, we prove that dual matrices of planar graphs have the same spectrum (up to multiplicities). We briefly comment on how this construction provides a refined formalization of Kirchhoff's mesh analysis of electrical circuits, which has lately been applied to generic thermodynamic networks.

A constrained maximization formulation to analyze deformation of fiber reinforced elastomeric actuators

NASA Astrophysics Data System (ADS)

Singh, Gaurav; Krishnan, Girish

2017-06-01

Fiber reinforced elastomeric enclosures (FREEs) are soft and smart pneumatic actuators that deform in a predetermined fashion upon inflation. This paper analyzes the deformation behavior of FREEs by formulating a simple calculus of variations problem that involves constrained maximization of the enclosed volume. The model accurately captures the deformed shape for FREEs with any general fiber angle orientation, and its relation with actuation pressure, material properties and applied load. First, the accuracy of the model is verified with existing literature and experiments for the popular McKibben pneumatic artificial muscle actuator with two equal and opposite families of helically wrapped fibers. Then, the model is used to predict and experimentally validate the deformation behavior of novel rotating-contracting FREEs, for which no prior literature exist. The generality of the model enables conceptualization of novel FREEs whose fiber orientations vary arbitrarily along the geometry. Furthermore, the model is deemed to be useful in the design synthesis of fiber reinforced elastomeric actuators for general axisymmetric desired motion and output force requirement.

Epibiotic Diatoms Are Universally Present on All Sea Turtle Species

PubMed Central

Majewska, Roksana; Lazo-Wasem, Eric A.; Nel, Ronel; Paladino, Frank V.; Rojas, Lourdes; Zardus, John D.; Pinou, Theodora

2016-01-01

The macro-epibiotic communities of sea turtles have been subject to growing interest in recent years, yet their micro-epibiotic counterparts are almost entirely unknown. Here, we provide the first evidence that diatoms are epibionts for all seven extant species of sea turtle. Using Scanning Electron Microscopy, we inspected superficial carapace or skin samples from a single representative of each turtle species. We distinguished 18 diatom taxa from these seven individuals, with each sea turtle species hosting at least two diatom taxa. We recommend that future research is undertaken to confirm whether diatom communities vary between sea turtle species and whether these diatom taxa are facultative or obligate commensals. PMID:27257972

Calibration of diatom-pH-alkalinity methodology for the interpretation of the sedimentary record in Emerald Lake Integrated watershed study. Final report, 6 May 1985-10 October 1986

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holmes, R.W.

1986-10-10

The present study was designed to establish quantitative relationships between lake air-equilibrated pH, alkalinity, and diatoms occurring in the surface sediments in high-elevation Sierra Nevada Lakes. These relationships provided the necessary information to develop predictive equations relating lake pH to the composition of surface-sediment diatom assemblages in 27 study lakes. Using the Hustedt diatom pH classification system, Index B of Renberg and Hellberg, and multiple linear regression analysis, two equations were developed which predict lake pH from the relative abundance of sediment diatoms occurring in each of four diatom pH groupings.

Fossil diatoms imply common cometary origin of space-dust and the Polonnaruwa meteorite

NASA Astrophysics Data System (ADS)

Miyake, N.; Wallis, M. K.; Wickramasinghe, N. C.

2013-09-01

IDPs collected in 2001 at 40km altitude by cryosamplers studied via scanning electron microscopy and EDX were found to contain siliceous fibres and whiskers, some isolated but often embedded in a mineral matrix. The newly-arrived Polonnaruwa meteorite gives strong evidence for the hypothesis that they are fragments of diatoms agglomerating on solar system icy bodies. Diatom frustules and even whole diatom skeletons are identifiable within the meteorite. Specimens of a siliceous exoskeleton with multiple spines/whiskers have also been found, thought to be freshwater diatoms. As diatoms are dependent on a source of nitrogenous organics, the siliceous whiskers within IDPs would be an indicator of a photosynthesizing ecosystem, probably on a comet.

Applications of diatoms as potential microalgae in nanobiotechnology.

PubMed

Jamali, Ali Akbar; Akbari, Fariba; Ghorakhlu, Mohamad Moradi; de la Guardia, Miguel; Yari Khosroushahi, Ahmad

2012-01-01

Diatoms are single cell eukaryotic microalgae, which present in nearly every water habitat make them ideal tools for a wide range of applications such as oil explora-tion, forensic examination, environmental indication, biosilica pattern generation, toxicity testing and eutrophication of aqueous ecosystems. Essential information on diatoms were reviewed and discussed towards impacts of diatoms on biosynthesis and bioremediation. In this review, we present the recent progress in this century on the application of diatoms in waste degradation, synthesis of biomaterial, biomineraliza-tion, toxicity and toxic effects of mineral elements evaluations. Diatoms can be considered as metal toxicity bioindicators and they can be applied for biomineralization, synthesis of biomaterials, and degradation of wastes.

A Guide to the Common Diatoms at Water Pollution Surveillance System Stations.

ERIC Educational Resources Information Center

Weber, Cornelius I.

This guide was developed by the United States Environmental Protection Agency (EPA) as a taxonomic reference for the identification of diatoms. The taxonomic information included consists of a generic key to the common genera of diatoms, a section illustrating 164 diatom species representing 43 common genera found at the Water Pollution…

Architecture and material properties of diatom shells provide effective mechanical protection

NASA Astrophysics Data System (ADS)

Hamm, Christian E.; Merkel, Rudolf; Springer, Olaf; Jurkojc, Piotr; Maier, Christian; Prechtel, Kathrin; Smetacek, Victor

2003-02-01

Diatoms are the major contributors to phytoplankton blooms in lakes and in the sea and hence are central in aquatic ecosystems and the global carbon cycle. All free-living diatoms differ from other phytoplankton groups in having silicified cell walls in the form of two `shells' (the frustule) of manifold shape and intricate architecture whose function and role, if any, in contributing to the evolutionary success of diatoms is under debate. We explored the defence potential of the frustules as armour against predators by measuring their strength. Real and virtual loading tests (using calibrated glass microneedles and finite element analysis) were performed on centric and pennate diatom cells. Here we show that the frustules are remarkably strong by virtue of their architecture and the material properties of the diatom silica. We conclude that diatom frustules have evolved as mechanical protection for the cells because exceptional force is required to break them. The evolutionary arms race between diatoms and their specialized predators will have had considerable influence in structuring pelagic food webs and biogeochemical cycles.

[Distribution of Diatoms in Main Sections of Urban District Rivers with Drowning-prone in Chengdu].

PubMed

Ni, Z X; Xie, Q; Yi, X F

2016-10-01

To explore the species distribution and constituent ratio of diatoms in main sections of urban district rivers where drowning occurs frequently in Chengdu. Total 39 water samples from the sampling points of 5 rivers （Jinjiang, Jinniu, Qingyang, Wuhou and Chenghua districts） in October 2014 were collected. The diatoms smear were made and the species distribution and constituent ratio of diatoms from the water samples were analyzed using biological microscope and acquisition system of digital microscope. Total 21 species of diatoms were detected in main sections of urban district rivers in Chengdu. Significant differences in the dominant diatom species and proportions of the different rivers were observed, and there were different species existed in all sampling points of the upstream, midstream and downstream of the rivers. The database of species map, species distribution and constituent ratio of diatoms in main sections of urban district rivers in Chengdu are preliminarily established, which has special meaning for the analysis and evaluation of falling location inference using diatoms test in case investigation. Copyright© by the Editorial Department of Journal of Forensic Medicine

Architecture and material properties of diatom shells provide effective mechanical protection.

PubMed

Hamm, Christian E; Merkel, Rudolf; Springer, Olaf; Jurkojc, Piotr; Maier, Christian; Prechtel, Kathrin; Smetacek, Victor

2003-02-20

Diatoms are the major contributors to phytoplankton blooms in lakes and in the sea and hence are central in aquatic ecosystems and the global carbon cycle. All free-living diatoms differ from other phytoplankton groups in having silicified cell walls in the form of two 'shells' (the frustule) of manifold shape and intricate architecture whose function and role, if any, in contributing to the evolutionary success of diatoms is under debate. We explored the defence potential of the frustules as armour against predators by measuring their strength. Real and virtual loading tests (using calibrated glass microneedles and finite element analysis) were performed on centric and pennate diatom cells. Here we show that the frustules are remarkably strong by virtue of their architecture and the material properties of the diatom silica. We conclude that diatom frustules have evolved as mechanical protection for the cells because exceptional force is required to break them. The evolutionary arms race between diatoms and their specialized predators will have had considerable influence in structuring pelagic food webs and biogeochemical cycles.

Review--Interactions between diatoms and stainless steel: focus on biofouling and biocorrosion.

PubMed

Landoulsi, J; Cooksey, K E; Dupres, V

2011-11-01

There is a considerable body of information regarding bacterially enhanced corrosion, however, this review focuses on diatoms (unicellular algae) whose contribution to biocorrosion is less well studied. The reasons why diatoms have been neglected in studies of biocorrosion in natural waters are discussed and the question whether diatoms should be considered as inert with respect of electrochemical processes is considered. A particular focus is given to the case of stainless steels (SS), which are widely used in variety of applications in natural waters. Basic information on the cell biology of diatoms is included in the review, particularly with respect to their ability to 'sense' and adhere to surfaces. Investigations at the nanoscale are reviewed as these studies provide information about the behavior of cells at interfaces. Recent advances include the use of atomic force microscopy (AFM), although only a few studies have been applied to diatoms. Regarding the electrochemical behavior of SS, the mechanisms by which diatoms influence the potential ennoblement process is discussed. Such studies reveal the association of diatoms, in addition to bacteria, with biocorrosion processes.

Interactions between Diatoms and Bacteria

PubMed Central

Amin, Shady A.; Parker, Micaela S.

2012-01-01

Summary: Diatoms and bacteria have cooccurred in common habitats for hundreds of millions of years, thus fostering specific associations and interactions with global biogeochemical consequences. Diatoms are responsible for one-fifth of the photosynthesis on Earth, while bacteria remineralize a large portion of this fixed carbon in the oceans. Through their coexistence, diatoms and bacteria cycle nutrients between oxidized and reduced states, impacting bioavailability and ultimately feeding higher trophic levels. Here we present an overview of how diatoms and bacteria interact and the implications of these interactions. We emphasize that heterotrophic bacteria in the oceans that are consistently associated with diatoms are confined to two phyla. These consistent bacterial associations result from encounter mechanisms that occur within a microscale environment surrounding a diatom cell. We review signaling mechanisms that occur in this microenvironment to pave the way for specific interactions. Finally, we discuss known interactions between diatoms and bacteria and exciting new directions and research opportunities in this field. Throughout the review, we emphasize new technological advances that will help in the discovery of new interactions. Deciphering the languages of diatoms and bacteria and how they interact will inform our understanding of the role these organisms have in shaping the ocean and how these interactions may change in future oceans. PMID:22933565

[Evaluation of three methods for forensic diatom test].

PubMed

Wang, Yuzhong; Zhao, Jian; Li, Peng; Hu, Sunlin; Wang, Huipin; Wang, Huijun; Liu, Chao

2015-03-01

To compare the efficacy of three methods for forensic diatom test, namely strong acid digestion-centrifuge enrichment-light microscopy (SD-CE-LM), microwave digestion-membrane filtration-automated scanning electron microscopy (MD-ME-SEM), and microwave digestion-membrane filtration-light microscopy (MD-MF-LM). Sixty samples were randomly divided into 3 groups for diatom test using three methods, and the sample preparation time, degree of digestion and recovery rate of diatoms were compared. The sample preparation time was the shortest with MD-MF-LM and the longest with SD-CE-LM (P<0.05). MD-ME-SEM and MD-MF-LM allowed more thorough tissue digestion than SD-CE-LM. MD-ME-SEM resulted in the highest total recovery rate of diatom, followed by MD-MF-LM and then by SD-CE-LM (P<0.05); the recover rate of different diatom species was the highest with MD-ME-SEM, followed by MD-MF-LM and SD-CE-LM (P<0.05). SD-CE-LM has a low recovery rate of diatoms especially for those with lengths shorter than 40 µm or densities less than 1/5. With a high recovery rate and accuracy in diatom test, MD-ME-SEM is suitable for diagnosis of suspected drowning cases. MD-MF-LM is highly efficient, sensitive and convenient for forensic diatom test.

Lake warming favours small-sized planktonic diatom species

PubMed Central

Winder, Monika; Reuter, John E.; Schladow, S. Geoffrey

2008-01-01

Diatoms contribute to a substantial portion of primary production in the oceans and many lakes. Owing to their relatively heavy cell walls and high nutrient requirements, planktonic diatoms are expected to decrease with climate warming because of reduced nutrient redistribution and increasing sinking velocities. Using a historical dataset, this study shows that diatoms were able to maintain their biovolume with increasing stratification in Lake Tahoe over the last decades; however, the diatom community structure changed. Increased stratification and reduced nitrogen to phosphorus ratios selected for small-celled diatoms, particularly within the Cyclotella genus. An empirical model showed that a shift in phytoplankton species composition and cell size was consistent within different depth strata, indicating that altered nutrient concentrations were not responsible for the change. The increase in small-celled species was sufficient to decrease the average diatom size and thus sinking velocity, which strongly influences energy transfer through the food web and carbon cycling. Our results show that within the diverse group of diatoms, small-sized species with a high surface area to volume ratio were able to adapt to a decrease in mixing intensity, supporting the hypotheses that abiotic drivers affect the size structure of planktonic communities and that warmer climate favours small-sized diatom cells. PMID:18812287

Using diatom assemblages to assess urban stream conditions

USGS Publications Warehouse

Walker, C.E.; Pan, Y.

2006-01-01

We characterized changes in diatom assemblages along an urban-to-rural gradient to assess impacts of urbanization on stream conditions. Diatoms, water chemistry, and physical variables of riffles at 19 urban and 28 rural stream sites were sampled and assessed during the summer base flow period. Near stream land use was characterized using GIS. In addition, one urban and one rural site were sampled monthly throughout a year to assess temporal variation of diatom assemblages between the urban and rural stream sites. Canonical correspondence analysis (CCA) showed that the 1st ordination axis distinctly separated rural and urban sites. This axis was correlated with conductivity (r = 0.75) and % near-stream commercial/industrial land use (r = 0.55). TWINSPAN classified all sites into four groups based on diatom assemblages. These diatom-based site groups were significantly different in water chemistry (e.g., conductivity, dissolved nutrients), physical habitat (e.g., % stream substrate as fines), and near-stream land use. CCA on the temporal diatom data set showed that diatom assemblages had high seasonal variation along the 2nd axis in both urban and rural sites, however, rural and urban sites were well separated along the 1st ordination axis. Our results suggest that changes in diatom assemblages respond to urban impacts on stream conditions. ?? Springer 2006.

Testing Prospects for Reliable Diatom Nanotechnology in Microgravity

NASA Technical Reports Server (NTRS)

Gordon, Richard; Hoover, Richard B.; Tuszynski, Jack A.; deLuis, Javier; Camp, Philip J.; Tiffany, Mary Ann; Nagy, Stephen S.; Lerner, Beatriz E.

2007-01-01

The worldwide effort to grow nanotechnology, rather than use lithography, focuses on diatoms, single cell eukaryotic algae with ornate silica shells, which can be replaced by oxides and ceramics, or reduced to elemental silicon, to create complex nanostructures with compositions of industrial and electronics importance. Diatoms produce an enormous variety of structures, some of which are microtubule dependent and perhaps sensitive to microgravity. The NASA Single Loop for Cell Culture (SLCC) for culturing and observing microorganisms permits inexpensive, low labor in-space experiments. We propose to send up to the International Space Station diatom cultures of the three diatom species whose genomes are being sequenced, plus the giant diatoms of Antarctica (up to 2 mm diameter for a single cell) and the unique colonial diatom, Bacillaria paradoxa. Bacillaria cells move against each other in partial synchrony, like a sliding deck of cards, by a microfluidics mechanism. Will normal diatoms have aberrant pattern and shape or motility compared to ground controls? The generation time is typically one day, so that many generations may be examined from one flight. Rapid, directed evolution may be possible running the SLCC as a compustat. The shell shapes and patterns are preserved in hard silica, so that the progress of normal and aberrant morphogenesis may be followed by drying samples on a moving filter paper "diatom tape recorder". With a biodiversity of 100,000 distinct species, diatom nanotechnology may offer a compact and portable nanotechnology toolkit for exploration anywhere.

Prospects for commercial production of diatoms

DOE PAGES

Wang, Jaw -Kai; Seibert, Michael

2017-01-18

In this paper, a simple procedure that portends the open-pond growth of commercially viable diatoms is discussed. We examined a number of topics relevant to the production and harvesting of diatoms as well as topics concerning the production of bioproducts from diatoms. Among the former topics, we show that it is currently possible to continuously grow diatoms and control the presence of invasive species without chemical toxins at an average annual yield of 132 MT dry diatoms ha -1 over a period of almost 5 years, while maintaining the dominancy of the optimal diatom species on a seasonal basis. Themore » dominant species varies during the year. The production of microalgae is essentially agriculture, but without the ability to control invasive species in the absence of herbicides and insecticides, pollution and production costs would be prohibitive. Among the latter topics are the discussions of whether it is better to produce lipids and then convert them to biofuels or maximize the production of diatom biomass and then convert it to biocrude products using, for example, hydrothermal processes. It is becoming increasingly evident that without massive public support, the commercial production of microalgal biofuels alone will remain elusive. While economically competitive production of biofuels from diatoms will be difficult, when priority is given to multiple high-value products, including wastewater treatment, and when biofuels are considered co-products in a systems approach to commercial production of diatoms, an economically competitive process will become more likely.« less

Transformation techniques for metabolic engineering of diatoms and haptophytes: current state and prospects.

PubMed

Velmurugan, Natarajan; Deka, Deepi

2018-05-01

Diatoms and haptophytes represent a key segment of the dominant phytoplankton communities that frequently form massive blooms in the photic zone of the ocean and are considered indicators of global climate changes. Diatoms and haptophytes also play a vital role in the biological carbon fixation in the carbon cycles. Carbon partitioning within diatoms and haptophytes possesses a wide range of chemical compounds and storage materials, such as lipids, carbohydrates, and chlorophyll. Among the marine microorganisms, diatoms and haptophytes have been recognized as promising sources of long- and very long-chain polyunsaturated fatty acids (PUFA). So far, a variety of approaches have been employed for genetic modification in the nuclei of diatoms and haptophytes. Studies on transformation and metabolic engineering in various intracellular genomes, such as chloroplast and mitochondria, are scarce. Particle bombardment, Agrobacterium and PEG-mediated gene transfer, and electroporation have been reported for foreign gene transformation into the diatoms and haptophytes. Antibiotics (G418 and chloramphenicol) and herbicides (zeocin, hygromycin, and norflurazon) have been successfully demonstrated as the best selection markers. Despite the availability of a wide range of molecular tools for foreign gene expression in microalgae, very few promoters (lhcf1, nr, h4, ef2, fcp, and pds) have been reported for diatoms and haptophytes. Therefore, in this review, we first summarize the significant progress that has been achieved in transgene expression in diatoms and haptophytes and highlight the importance and availability of recently developed novel tools that are suitable for transgenic expression in diatoms and haptophytes.

Prospects for commercial production of diatoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jaw -Kai; Seibert, Michael

In this paper, a simple procedure that portends the open-pond growth of commercially viable diatoms is discussed. We examined a number of topics relevant to the production and harvesting of diatoms as well as topics concerning the production of bioproducts from diatoms. Among the former topics, we show that it is currently possible to continuously grow diatoms and control the presence of invasive species without chemical toxins at an average annual yield of 132 MT dry diatoms ha -1 over a period of almost 5 years, while maintaining the dominancy of the optimal diatom species on a seasonal basis. Themore » dominant species varies during the year. The production of microalgae is essentially agriculture, but without the ability to control invasive species in the absence of herbicides and insecticides, pollution and production costs would be prohibitive. Among the latter topics are the discussions of whether it is better to produce lipids and then convert them to biofuels or maximize the production of diatom biomass and then convert it to biocrude products using, for example, hydrothermal processes. It is becoming increasingly evident that without massive public support, the commercial production of microalgal biofuels alone will remain elusive. While economically competitive production of biofuels from diatoms will be difficult, when priority is given to multiple high-value products, including wastewater treatment, and when biofuels are considered co-products in a systems approach to commercial production of diatoms, an economically competitive process will become more likely.« less

An efficient screening method for the isolation of heterotrophic bacteria influencing growth of diatoms under photoautotrophic conditions.

PubMed

Zecher, Karsten; Jagmann, Nina; Seemann, Philipp; Philipp, Bodo

2015-12-01

Interactions between photoautotrophic diatoms and heterotrophic bacteria are important for the biogeochemical C-cycle in the oceans. Additionally, biofilms formed by diatoms and bacteria are the initiating step of biofouling processes, which causes high costs in shipping. Despite this ecological and economical importance, the knowledge about biochemical and molecular mechanisms underlying these interkingdom interactions is relatively small. For analyzing these mechanisms, laboratory model systems are required. In this study, an efficient screening method for isolating bacteria influencing photoautotrophic diatom growth was established. First, diatom cultures of Phaeodactylum tricornutum and Thalassiosira pseudonana were made axenic by applying β-lactam antibiotics. Second, a non-invasive method for measuring growth of multiple parallel diatom cultures by chlorophyll fluorescence was established. This method allowed semi-quantitative chlorophyll determination of cultures with up to 3 μg (chlorophyll) ml(-1). Axenic diatom cultures were then used for enriching bacteria and led to the isolation of 24 strains influencing growth of both diatom strains in various ways. For example, Rheinheimera sp. strain Tn16 inhibited growth of T. pseudonana, while it stimulated growth and cell aggregation of P. tricornutum. Thus, this screening method is appropriate for isolating heterotrophic bacteria showing different interactions with different diatom species ranging from synergistic to antagonistic. In consecutive applications, this method will be useful to screen for bacterial mutants with altered phenotypes regarding the influence on diatom growth. Copyright © 2015 Elsevier B.V. All rights reserved.

What if the Diatoms of the Deep Chlorophyll Maximum Can Ascend?

NASA Astrophysics Data System (ADS)

Villareal, T. A.

2016-02-01

Buoyancy regulation is an integral part of diatom ecology via its role in sinking rates and is fundamental to understanding their distribution and abundance. Numerous studies have documented the effects of size and nutrition on sinking rates. Many pelagic diatoms have low intrinsic sinking rates when healthy and nutrient-replete (< 1-2 meters per day). Physiological control of buoyancy via ion regulation and osmolyte control can easily result in cell sap densities less than seawater, resulting in near-zero sinking rates across a large size spectrum of diatoms as well as positive buoyancy in giant diatoms with their low surface:volume ratio. Ascent by smaller diatoms is much less described although predicted in cells as small as 200 cubic microns. Decreased sedimentation rates have long been linked to formation of layers in the water column, particularly at the low light and nutricline conditions of the deep chlorophyll maximum. The potential for ascending behavior adds an additional layer of complexity by allowing both active depth regulation similar to that observed in flagellated taxa and upward transport by some fraction of deep euphotic zone diatom blooms supported by nutrient injection. In this talk, I review the data documenting positive buoyancy in small diatoms, offer direct visual evidence of ascending behavior in common diatoms typical of both oceanic and coastal zones, and note the characteristics of sinking rate distributions within a single species. Buoyancy control leads to bidirectional movement at similar rates across a wide size spectrum of diatoms although the frequency of ascending behavior may be only a small portion of the individual species' abundance. While much remains to be learned, the paradigm of unidirectional downward movement by diatoms is both inaccurate and an oversimplification.

First account of apochlorotic diatoms from intertidal sand of a south Florida beach

NASA Astrophysics Data System (ADS)

Blackburn, Michele V.; Hannah, Fiona; Rogerson, Andrew

2009-10-01

During the period January to December 2004, monthly intertidal sand samples were collected from John U. Lloyd State Park beach, Florida. This study is the first to report on spatial and temporal distributions of heterotrophic (apochlorotic) diatoms in a sub-tropical beach, or indeed any sandy beach. Two non-pigmented, apochlorotic diatom morphotypes (strains III and IV) were consistently isolated from two intertidal beach sites and neither conformed to the morphologies of described species. Apochlorotic diatoms were found throughout the year and formed significant peaks in April, attaining total diatom counts of 71.1 and 94.9 cells g -1 wet sand, for the upper tidal zone and lower tidal zone, respectively. Valve morphology is described in detail for the two diatom morphotypes isolated from the beach sites (strains III and IV). Growth responses to changes in salinity (reflecting those of the intertidal zone) were examined in the laboratory for these diatoms. Both morphotypes were euryhaline, tolerating salinities between 10 and 50, and maximum growth rates were achieved at salinities between 20 and 40. Diatoms grew equally well whether grown in the light or the dark and showed no evidence of pigments when viewed by epifluorescence microscopy. The ability of diatoms to burrow into agar and carrageenan at different concentrations was tested. Both morphotypes were observed to develop burrows through non-nutrient agar up to twice the standard concentration (30 g agar l -1). The ease with which these heterotrophic diatoms formed burrows suggests that they were digesting these complex carbohydrates (i.e. phycocolloids) as a nutrient source. Strain IV, however, failed to burrow in a different phycocolloid, carrageenan. Similar degradative actions in the field might have implications for the breakdown of recalcitrant materials or allow diatoms to effectively compete with bacteria for carbon and nutrients.

Diatom community structure on in-service cruise ship hulls.

PubMed

Hunsucker, Kelli Zargiel; Koka, Abhishek; Lund, Geir; Swain, Geoffrey

2014-10-01

Diatoms are an important component of marine biofilms found on ship hulls. However, there are only a few published studies that describe the presence and abundance of diatoms on ships, and none that relate to modern ship hull coatings. This study investigated the diatom community structure on two in-service cruise ships with the same cruise cycles, one coated with an antifouling (AF) system (copper self-polishing copolymer) and the other coated with a silicone fouling-release (FR) system. Biofilm samples were collected during dry docking from representative areas of the ship and these provided information on the horizontal and vertical zonation of the hull, and intact and damaged coating and niche areas. Diatoms from the genera Achnanthes, Amphora and Navicula were the most common, regardless of horizontal ship zonation and coating type. Other genera were abundant, but their presence was more dependent on the ship zonation and coating type. Samples collected from damaged areas of the hull coating had a similar community composition to undamaged areas, but with higher diatom abundance. Diatom fouling on the niche areas differed from that of the surrounding ship hull and paralleled previous studies that investigated differences in diatom community structure on static and dynamically exposed coatings; niche areas were similar to static immersion and the hull to dynamic immersion. Additionally, diatom richness was greater on the ship with the FR coating, including the identification of several new genera to the biofouling literature, viz. Lampriscus and Thalassiophysa. These results are the first to describe diatom community composition on in-service ship hulls coated with a FR system. This class of coatings appears to have a larger diatom community compared to copper-based AF systems, with new diatom genera that have the ability to stick to ship hulls and withstand hydrodynamic forces, thus creating the potential for new problematic species in the biofilm.

Selective and context-dependent effects of chemical stress across trophic levels at the basis of marine food webs.

PubMed

Mensens, Christoph; De Laender, Frederik; Janssen, Colin R; Rivera, Frances Camille; Sabbe, Koen; De Troch, Marleen

2018-04-26

Human activities increasingly impact the functioning of marine food webs, but anthropogenic stressors are seldom included in ecological study designs. Diet quality, as distinct from just diet quantity, has moreover rarely been highlighted in food web studies in a stress context. We measured the effects of metal and pesticide stress (copper and atrazine) on the contribution of a benthic intertidal diatom community to two processes that are key to the functioning of intertidal systems: biomass (diet quantity) and lipid (diet quality) production. We then examined if stressors affected diatom functioning by selectively targeting the species contributing most to functioning (selective stress effects) or by changing the species' functional contribution (context-dependent effects). Finally, we tested if stress-induced changes in diet quality altered the energy flow to the diatoms' main grazers (harpacticoid copepods). Diatom diet quantity was reduced by metal stress but not by low pesticide levels due to the presence of an atrazine-tolerant, mixotrophic species. Selective effects of the pesticide reduced diatom diet quality by 60% and 75% at low and high pesticide levels respectively, by shifting diatom community structure from dominance by lipid-rich species toward dominance by an atrazine-tolerant, but lipid-poor, species. Context-dependent effects did not affect individual diatom lipid content at low levels of both stressors, but caused diatoms to lose 40% of their lipids at high copper stress. Stress-induced changes in diet quality predicted the energy flow from the diatoms to their copepod consumers, which lost half of their lipids when feeding on diatoms grown under low and high pesticide and high metal stress. Selective pesticide effects were a more important threat for trophic energy transfer than context-dependent effects of both stressors, with shifts in diatom community structure affecting the energy flow to their copepod grazers at stress levels where no changes in diatom lipid content were detected. © 2018 by the Ecological Society of America.

Do diatoms percolate through soil and can they be used for tracing the origin of runoff?

NASA Astrophysics Data System (ADS)

De Graaf, Lenka; Cammeraat, Erik; Pfister, Laurent; Wetzel, Carlos; Klaus, Julian; Hissler, Christophe

2015-04-01

Tracers are widely used to study the movement of water in a catchment. Because of depletion of scientific possibilities with most common tracer types, we proposed the use of diatoms as a natural tracer. Paradoxical results on the contribution of surface runoff to the storm hydrograph were obtained in pioneer research on this idea. Diatom transport via the subsurface flow to the stream would explain this paradox. Prerequisite for this is vertical transport of diatoms through soils, which is the topic of this study. Emphasis is on percolation behavior (speed of percolation, speed of percolation over time, and species distribution) of Pseudostaurosira sp. and Melosira sp. (Bacillariophyceae) through undisturbed soil columns of contrasting substrates. Co-objective is to study the flowpaths of water through the soil columns. Natural undisturbed soil columns were sampled in the Attert basin (Luxembourg) on schist, marl and sandstone substrates. Rain simulation experiments were performed to study vertical diatom transport. Rhodamine dye experiments were carried out to gain insight in the active flowpaths of water, and breakthrough experiments were performed to study the responses of the soil columns to applied water. Diatoms were transported through the soil columns of the three substrates. A vast majority of diatom percolation took place within the first 15 minutes, percolation hereafter was marginal but nevertheless present. Peaks in diatom percolation corresponded with a high flux caused by the addition of the diatom culture, but seepage of diatoms along the sides is unlikely according to the species distribution and the rhodamine dye experiment. Pseudostaurosira sp. percolated significantly better than Melosira sp. Significantly more diatoms percolated through the marl columns compared to the schist columns and variance within the sandstone group was very high. Absolute differences between substrates however, were marginal. Most preferential flowpaths were observed in the marl columns, indicating highest active macroporosity in these columns. Although the sample size of this study was small, it is suspected that the highest diatom percolation percentages of the marl columns is linked to its greater macroporosity and most importantly, diatoms can percolate through soil (macro-) pores.

Robustness of the filamentation instability for asymmetric plasma shells collision in arbitrarily oriented magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bret, A.

2013-10-15

The filamentation instability triggered when two counter streaming plasma shells overlap appears to be the main mechanism by which collisionless shocks are generated. It has been known for long that a flow aligned magnetic field can completely suppress this instability. In a recent paper [Phys. Plasmas 18, 080706 (2011)], it was demonstrated in two dimensions that for the case of two cold, symmetric, relativistically colliding shells, such cancellation cannot occur if the field is not perfectly aligned. Here, this result is extended to the case of two asymmetric shells. The filamentation instability appears therefore as an increasingly robust mechanism tomore » generate shocks.« less

Three-dimensional control of crystal growth using magnetic fields

NASA Astrophysics Data System (ADS)

Dulikravich, George S.; Ahuja, Vineet; Lee, Seungsoo

1993-07-01

Two coupled systems of partial differential equations governing three-dimensional laminar viscous flow undergoing solidification or melting under the influence of arbitrarily oriented externally applied magnetic fields have been formulated. The model accounts for arbitrary temperature dependence of physical properties including latent heat release, effects of Joule heating, magnetic field forces, and mushy region existence. On the basis of this model a numerical algorithm has been developed and implemented using central differencing on a curvilinear boundary-conforming grid and Runge-Kutta explicit time-stepping. The numerical results clearly demonstrate possibilities for active and practically instantaneous control of melt/solid interface shape, the solidification/melting front propagation speed, and the amount and location of solid accrued.

Coherent Perfect Rotation: The conservative analogue of CPA

NASA Astrophysics Data System (ADS)

Crescimanno, Michael; Dawson, Nathan; Andrews, James

2012-06-01

The two classes of conservative, linear, optical rotary effects (optical activity and Faraday rotation) are distinguished by their behavior under time reversal. In analogy with coherent perfect absorption (CPA) resonances, where counter-propagating light fields are completely converted into other degrees of freedom, we show that in a linear conservative medium only time-odd (Faraday) rotation is capable of coherent perfect rotation, by which we mean the complete transfer of any arbitrarily oriented polarization of light into the other orthogonal polarization via the application of phased counter-propagating light fields. This contributes to the understanding of the importance of time reversal symmetry in perfect mode conversion that may be of use in optical device design.

Computer program: Jet 3 to calculate the large elastic plastic dynamically induced deformations of free and restrained, partial and/or complete structural rings

NASA Technical Reports Server (NTRS)

Wu, R. W.; Witmer, E. A.

1972-01-01

A user-oriented FORTRAN 4 computer program, called JET 3, is presented. The JET 3 program, which employs the spatial finite-element and timewise finite-difference method, can be used to predict the large two-dimensional elastic-plastic transient Kirchhoff-type deformations of a complete or partial structural ring, with various support conditions and restraints, subjected to a variety of initial velocity distributions and externally-applied transient forcing functions. The geometric shapes of the structural ring can be circular or arbitrarily curved and with variable thickness. Strain-hardening and strain-rate effects of the material are taken into account.

Responses of diatom communities to hydrological processes during rainfall events

NASA Astrophysics Data System (ADS)

Wu, Naicheng; Faber, Claas; Ulrich, Uta; Fohrer, Nicola

2015-04-01

The importance of diatoms as a tracer of hydrological processes has been recently recognized (Pfister et al. 2009, Pfister et al. 2011, Tauro et al. 2013). However, diatom variations in a short-term scale (e.g., sub-daily) during rainfall events have not been well documented yet. In this study, rainfall event-based diatom samples were taken at the outlet of the Kielstau catchment (50 km2), a lowland catchment in northern Germany. A total of nine rainfall events were caught from May 2013 to April 2014. Non-metric multidimensional scaling (NMDS) revealed that diatom communities of different events were well separated along NMDS axis I and II, indicating a remarkable temporal variation. By correlating water level (a proxy of discharge) and different diatom indices, close relationships were found. For example, species richness, biovolume (μm3), Shannon diversity and moisture index01 (%, classified according to van Dam et al. 1994) were positively related with water level at the beginning phase of the rainfall (i.e. increasing limb of discharge peak). However, in contrast, during the recession limb of the discharge peak, diatom indices showed distinct responses to water level declines in different rainfall events. These preliminary results indicate that diatom indices are highly related to hydrological processes. The next steps will include finding out the possible mechanisms of the above phenomena, and exploring the contributions of abiotic variables (e.g., hydrologic indices, nutrients) to diatom community patterns. Based on this and ongoing studies (Wu et al. unpublished data), we will incorporate diatom data into End Member Mixing Analysis (EMMA) and select the tracer set that is best suited for separation of different runoff components in our study catchment. Keywords: Diatoms, Rainfall event, Non-metric multidimensional scaling, Hydrological process, Indices References: Pfister L, McDonnell JJ, Wrede S, Hlúbiková D, Matgen P, Fenicia F, Ector L, Hoffmann L. 2009. The rivers are alive: on the potential for diatoms as a tracer of water source and hydrological connectivity. Hydrological Processes 23: 2841-2845. Pfister L, Wetzel CE, Martínez-Carreras N, Frentress J, Ector L, Hoffmann L, McDonnell JJ. 2011. Do diatoms run downhill? Using biodiversity of terrestrial and aquatic diatoms to identify hydrological connectivity between aquatic zones in Luxembourg. AGU Fall Meeting. Tauro F, Martínez-Carreras N, Wetzel CE, Hissler C, Barnich F, Frentress J, Ector L, Hoffmann L, McDonnell JJ, Pfister L. 2013. Fluorescent diatoms as hydrological tracers: a proof of concept percolation experiment. EGU abstract, EGU2013-7687-4. van Dam H, Mertens A, Sinkeldam J. 1994. A coded checklist and ecological indicator values of freshwater diatoms from the Netherlands. Netherlands Journal of Aquatic Ecology 28:117-133.

Paleoceanographic, and paleoclimatic constraints on the global Eocene diatom and silicoflagellate record

USGS Publications Warehouse

Barron, John A.; Stickley, Catherine E.; Bukry, David

2015-01-01

Tabulation of the first and last occurrences of 132 biostratigraphically-important diatoms suggests increased species turnover during the latest Paleocene to earliest Eocene that may be in part due to a monographic effect. An increasing rate of evolution of new diatom species between ~ 46 and 43 Ma and after ~ 40 Ma coincides respectively with the widespread expansion of diatom deposition in the Atlantic and with an increased pole-to-equator thermal gradient that witnessed the expansion of diatoms in high latitude oceans and coastal upwelling settings.

An integrated approach for probing the structure and mechanical properties of diatoms: Toward engineered nanotemplates.

PubMed

Moreno, Miguel Diaz; Ma, Kaka; Schoenung, Julie; Dávila, Lilian P

2015-10-01

The wide variety of diatom frustule shapes and intricate architectures provide viable prototypes to guide the design and fabrication of nanodevices and nanostructured materials for applications ranging from sensors to nanotemplates. In this study, a combined experimental-simulation method was developed to probe the porous structure and mechanical behavior of two distinct marine diatom species, Coscinodiscus sp. (centric) and Synedra sp. (pennate), through ambient nanoindentation and finite element method analysis. These diatom frustule dimensions differed largely depending on diatom species with pore diameters d ranging from 0.3 to 3.0 μm. Young's modulus E and hardness H measurements of the diatom frustules were obtained via nanoindentation experiments. These values varied depending on diatom species (E between 1.1-10.6 GPa, H between 0.10-1.03 GPa for the Coscinodiscus sp.; and E between 13.7-18.6 GPa, H between 0.85-1.41 GPa for the Synedra sp.). Additionally, the mechanical response of diatom structures to uniform compression was examined. Predictive simulations were performed on the aforementioned diatom frustules, as well as another diatom structure (pennate Fragilariopsis kerguelensis), to correlate the mechanical response with specific morphology variables (e.g., pore or slit sizes). Results from calculated von Mises stress and displacement distributions unveil unique information on the effect that uniform loads have on these frustules, which can aid the design of tailored nanotemplates. A correlation between mechanical properties and porosity was established for selected frustules, and reported for the first time in this study. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability.

PubMed

Marchetti, Adrian; Schruth, David M; Durkin, Colleen A; Parker, Micaela S; Kodner, Robin B; Berthiaume, Chris T; Morales, Rhonda; Allen, Andrew E; Armbrust, E Virginia

2012-02-07

In vast expanses of the oceans, growth of large phytoplankton such as diatoms is limited by iron availability. Diatoms respond almost immediately to the delivery of iron and rapidly compose the majority of phytoplankton biomass. The molecular bases underlying the subsistence of diatoms in iron-poor waters and the plankton community dynamics that follow iron resupply remain largely unknown. Here we use comparative metatranscriptomics to identify changes in gene expression associated with iron-stimulated growth of diatoms and other eukaryotic plankton. A microcosm iron-enrichment experiment using mixed-layer waters from the northeastern Pacific Ocean resulted in increased proportions of diatom transcripts and reduced proportions of transcripts from most other taxa within 98 h after iron addition. Hundreds of diatom genes were differentially expressed in the iron-enriched community compared with the iron-limited community; transcripts of diatom genes required for synthesis of photosynthesis and chlorophyll components, nitrate assimilation and the urea cycle, and synthesis of carbohydrate storage compounds were significantly overrepresented. Transcripts of genes encoding rhodopsins in eukaryotic phytoplankton were significantly underrepresented following iron enrichment, suggesting rhodopsins help cells cope with low-iron conditions. Oceanic diatoms appear to display a distinctive transcriptional response to iron enrichment that allows chemical reduction of available nitrogen and carbon sources along with a continued dependence on iron-free photosynthetic proteins rather than substituting for iron-containing functional equivalents present within their gene repertoire. This ability of diatoms to divert their newly acquired iron toward nitrate assimilation may underlie why diatoms consistently dominate iron enrichments in high-nitrate, low-chlorophyll regions.

DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior

PubMed Central

Vasselon, Valentin; Ballorain, Katia; Carpentier, Alice; Wetzel, Carlos E.; Ector, Luc; Bouchez, Agnès; Rimet, Frédéric

2018-01-01

Sea turtles are distributed in tropical and subtropical seas worldwide. They play several ecological roles and are considered important indicators of the health of marine ecosystems. Studying epibiotic diatoms living on turtle shells suggestively has great potential in the study of turtle behavior because diatoms are always there. However, diatom identification at the species level is time consuming, requires well-trained specialists, and there is a high probability of finding new taxa growing on turtle shells, which makes identification tricky. An alternative approach based on DNA barcoding and high throughput sequencing (HTS), metabarcoding, has been developed in recent years to identify species at the community level by using a DNA reference library. The suitabilities of morphological and molecular approaches were compared. Diatom assemblages were sampled from seven juvenile green turtles (Chelonia mydas) from Mayotte Island, France. The structures of the epibiotic diatom assemblages differed between both approaches. This resulted in different clustering of the turtles based on their diatom communities. Metabarcoding allowed better discrimination between turtles based on their epibiotic diatom assemblages and put into evidence the presence of a cryptic diatom diversity. Microscopy, for its part, provided more ecological information of sea turtles based on historical bibliographical data and the abundances of ecological guilds of the diatom species present in the samples. This study shows the complementary nature of these two methods for studying turtle behavior. PMID:29659610

The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms.

PubMed

Young, Jodi N; Hopkinson, Brian M

2017-06-01

Diatoms are a diverse group of unicellular algae that contribute significantly to global photosynthetic carbon fixation and export in the modern ocean, and are an important source of microfossils for paleoclimate reconstructions. Because of their importance in the environment, diatoms have been a focus of study on the physiology and ecophysiology of carbon fixation, in particular their CO2-concentrating mechanisms (CCMs) and Rubisco characteristics. While carbon fixation in diatoms is not as well understood as in certain model aquatic photoautotrophs, a greater number of species have been examined in diatoms. Recent work has highlighted a large diversity in the function, physiology, and kinetics of both the CCM and Rubisco between different diatom species. This diversity was unexpected since it has generally been assumed that CCMs and Rubiscos were similar within major algal lineages as the result of selective events deep in evolutionary history, and suggests a more recent co-evolution between the CCM and Rubisco within diatoms. This review explores our current understanding of the diatom CCM and highlights the diversity of both the CCM and Rubisco kinetics. We will suggest possible environmental, physiological, and evolutionary drivers for the co-evolution of the CCM and Rubisco in diatoms. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior.

PubMed

Rivera, Sinziana F; Vasselon, Valentin; Ballorain, Katia; Carpentier, Alice; Wetzel, Carlos E; Ector, Luc; Bouchez, Agnès; Rimet, Frédéric

2018-01-01

Sea turtles are distributed in tropical and subtropical seas worldwide. They play several ecological roles and are considered important indicators of the health of marine ecosystems. Studying epibiotic diatoms living on turtle shells suggestively has great potential in the study of turtle behavior because diatoms are always there. However, diatom identification at the species level is time consuming, requires well-trained specialists, and there is a high probability of finding new taxa growing on turtle shells, which makes identification tricky. An alternative approach based on DNA barcoding and high throughput sequencing (HTS), metabarcoding, has been developed in recent years to identify species at the community level by using a DNA reference library. The suitabilities of morphological and molecular approaches were compared. Diatom assemblages were sampled from seven juvenile green turtles (Chelonia mydas) from Mayotte Island, France. The structures of the epibiotic diatom assemblages differed between both approaches. This resulted in different clustering of the turtles based on their diatom communities. Metabarcoding allowed better discrimination between turtles based on their epibiotic diatom assemblages and put into evidence the presence of a cryptic diatom diversity. Microscopy, for its part, provided more ecological information of sea turtles based on historical bibliographical data and the abundances of ecological guilds of the diatom species present in the samples. This study shows the complementary nature of these two methods for studying turtle behavior.

Influence of diatom diversity on the ocean biological carbon pump

NASA Astrophysics Data System (ADS)

Tréguer, Paul; Bowler, Chris; Moriceau, Brivaela; Dutkiewicz, Stephanie; Gehlen, Marion; Aumont, Olivier; Bittner, Lucie; Dugdale, Richard; Finkel, Zoe; Iudicone, Daniele; Jahn, Oliver; Guidi, Lionel; Lasbleiz, Marine; Leblanc, Karine; Levy, Marina; Pondaven, Philippe

2018-01-01

Diatoms sustain the marine food web and contribute to the export of carbon from the surface ocean to depth. They account for about 40% of marine primary productivity and particulate carbon exported to depth as part of the biological pump. Diatoms have long been known to be abundant in turbulent, nutrient-rich waters, but observations and simulations indicate that they are dominant also in meso- and submesoscale structures such as fronts and filaments, and in the deep chlorophyll maximum. Diatoms vary widely in size, morphology and elemental composition, all of which control the quality, quantity and sinking speed of biogenic matter to depth. In particular, their silica shells provide ballast to marine snow and faecal pellets, and can help transport carbon to both the mesopelagic layer and deep ocean. Herein we show that the extent to which diatoms contribute to the export of carbon varies by diatom type, with carbon transfer modulated by the Si/C ratio of diatom cells, the thickness of the shells and their life strategies; for instance, the tendency to form aggregates or resting spores. Model simulations project a decline in the contribution of diatoms to primary production everywhere outside of the Southern Ocean. We argue that we need to understand changes in diatom diversity, life cycle and plankton interactions in a warmer and more acidic ocean in much more detail to fully assess any changes in their contribution to the biological pump.

Diatom biostratigraphy and paleoecology of the type section of the Luisian Stage, central California

USGS Publications Warehouse

Baldauf, Jack G.; Barron, John A.

1982-01-01

Diatoms from the type section of the Luisian Stage in central California correlate with the lowermost part of the Denticulopsis lauta Zone through the lower part of subzone "a" of the Denticulopsis hustedtii-D. lauta Zone and are early Middle Miocene in age (about 6.0 to 14.0 Ma), Rocks assigned to the Luisian Stage by benthic foraminifers elsewhere in California exhibit little diachroneity in terms of diatom biostratigraphy, however, detailed studies of boundaries have not been done. Planktic diatoms dominate the assemblages, although an increase in benthic and tychopelagic diatoms in the overlying Hames Member of the Monterey Formation probably reflects shoaling. A cooling trend is suggested by diatom assemblages in the upper part of the section and is most marked near the top of the type Luisian. This cooling trend is supported by data elsewhere in the Pacific Basin as well as by both megafossil and microfossil studies in California. One hundred four diatom taxa are documented, and one new species, Coscinodiscus volutus Baldauf, is described.

Potential forensic biogeographic application of diatom colony consistency analysis employing pyrosequencing profiles of the 18S rDNA V7 region.

PubMed

Zhao, Yuancun; Chen, Xiaogang; Yang, Yiwen; Zhao, Xiaohong; Zhang, Shu; Gao, Zehua; Fang, Ting; Wang, Yufang; Zhang, Ji

2018-05-07

Diatom examination has always been used for the diagnosis of drowning in forensic practice. However, traditional examination of the microscopic features of diatom frustules is time-consuming and requires taxonomic expertise. In this study, we demonstrate a potential DNA-based method of inferring suspected drowning site using pyrosequencing (PSQ) of the V7 region of 18S ribosome DNA (18S rDNA) as a diatom DNA barcode. By employing a sparse representation-based AdvISER-M-PYRO algorithm, the original PSQ signals of diatom DNA mixtures were deciphered to determine the corresponding taxa of the composite diatoms. Additionally, we evaluated the possibility of correlating water samples to collection sites by analyzing the PSQ signal profiles of diatom mixtures contained in the water samples via multidimensional scaling. The results suggest that diatomaceous PSQ profile analysis could be used as a cost-effective method to deduce the geographical origin of an environmental bio-sample.

Antarctic climate cooling and response of diatoms in glacial meltwater streams

USGS Publications Warehouse

Esposito, R.M.M.; Horn, S.L.; McKnight, Diane M.; Cox, M.J.; Grant, M.C.; Spaulding, S.A.; Doran, P.T.; Cozzetto, K.D.

2006-01-01

To understand biotic responses to an Antarctic cooling trend diatom samples from glacial meltwater streams in the McMurdo Dry Valleys, the largest ice-free area in Antarctica. Diatoms are abundant in these streams, and 24 of 40 species have only been found in the Antarctic. The percentage of these Antarctic diatom species increased with decreasing annual stream flow and increasing harshness of the stream habitat. The species diversity of assemblages reached a maximum when the Antarctic species accounted for 40-60% of relative diatom abundance. Decreased solar radiation and air-temperatures reduce annual stream flow, raising the dominance of these Antarctic species to levels above 60%. Thus, cooling favors the Antarctic species, and lowers diatom species diversity in this region. Copyright 2006 by the American Geophysical Union.

Miocene non-marine diatoms from the western Cordillera basins of northern Peru

USGS Publications Warehouse

Fourtanier, E.; Gasse, F.; Bellier, O.; Bonhomme, M.G.; Robles, I.

1993-01-01

Diatom assemblages are documented from diatomite layers of two Miocene fluvio-lacustrine units from the basins of the western Cordillera of northern Peru: the Namora Formation and the Cajabamba Formation. Emphasis is given to taxa of particular stratigraphic interest. The diatom assemblages indicate for the Namora Formation the occurrence of swampy conditions with very dilute, low alkalinity water. The diatom assemblages of the Cajabamba Formation reflect the occurrence of fresh, slightly alkaline, eutrophic lakes with deep water in some samples, and swampy conditions with relatively high salt content in other samples. The Namora formation is late Miocene in age based on the diatom assemblages and radiometric analyses. The diatom layers of the Cajabamba Formation are dated as late middle to early late Miocene. -from Authors

The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ambrust, E.V.; Berges, J.; Bowler, C.

2004-09-01

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in themore » marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different evolutionary history from the higher plants that dominate photosynthesis on land. Higher plants and green, red and glaucophyte algae are derived from a primary endosymbiotic event in which a non-photosynthetic eukaryote acquired a chloroplast by engulfing (or being invaded by) a prokaryotic cyanobacterium. In contrast, dominant bloom-forming eukaryotic phytoplankton in the ocean, such as diatoms and haptophytes, were derived by secondary endosymbiosis whereby a non-photosynthetic eukaryote acquired a chloroplast by engulfing a photosynthetic eukaryote, probably a red algal endosymbiont (Fig. 1). Each endosymbiotic event led to new combinations of genes derived from the hosts and endosymbionts (7). Prior to this project, relatively few diatom genes had been sequenced, few chromosome numbers were known, and genetic maps did not exist (8). The ecological and evolutionary importance of diatoms motivated our sequencing and analysis of the nuclear, plastid, and mitochondrial genomes of the marine centric diatom Thalassiosira pseudonana.« less

Soviet chemical laser research: pulsed lasers. Report for 1963--1970

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ksander, Y.

1971-11-01

The document reviews Soviet work on pulsed chemical lasers published in the open litarature in 1963-1970. Whereas U. S. research combines the approaches of physics, quantum electrodynamics, and aerodynamics, Soviet laser research is heavily (and expertly) oriented to understanding the chemical reactions. They prefer pulsed to cw systems, concentrating on kinetics of vibrationally excited diatomic systems. The documents describe gas lasers with discharge, photolytic, and other initiation and includes research on HN/sub 3/ + CO/sub 2/ mixtures, and means of controlling reaction rates by resonant coupling and selective heating. The report also proposes a laser based on photorecombination of atoms.

Sampler collection gadget for epilithic diatoms.

PubMed

Salomoni, S E; Torgan, L C; Rocha, O

2007-11-01

This work present a new gadget for sampling epilithic diatoms from both lentic and lotic enviroments. The sampler consists of a polystyrene cylinder, left to float on the surface of the water, to which stone substrates are attached. This epilithic diatom sampler (EDS) can be used to detect spatial and temporal richness and density variation in the study of the diatom community, as well as in water quality monitoring.

A First Look at Oxygen and Silicon Isotope Variations in Diatom Silica from a Pliocene Antarctic Marine Sediment Core

NASA Astrophysics Data System (ADS)

Abbott, T.; Dodd, J. P.; Hackett, H.; Scherer, R. P.

2016-02-01

Coupled oxygen (δ18O) and silicon (δ30Si) isotope variations in diatom silica (opal-A) are increasingly used as a proxy to reconstruct paleoenvironmental conditions (water temperatures, water mass mixing, nutrient cycling) in marine environments. Diatom silica is a particularly significant paleoenvironmental proxy in high latitude environments, such as the Southern Ocean, where diatom blooms are abundant and diatom frustules are well preserved in the sediment. The Andrill-1B (AND-1B) sediment core from the Ross Sea (Antarctica) preserves several Pliocene ( 4.5 Ma) age diatomite units. Here we present preliminary δ18O and δ30Si values for a diatomite subunit in the AND-1B sediment core. Initial isotope values for the AND-1B diatoms silica record relatively high variability (range δ18O: 36.3‰ to 39.9‰) that could be interpreted as large-scale changes in the water temperature and/or freshwater mixing in the Ross Sea; however, a significant concern with marine sediment of this age is isotope fractionation during diagenesis and the potential formation of opal-CT lepispheres. The effects of clay contamination on the diatom silica δ18O values have been addressed through sample purification and quantified through chemical and physical analyses of the diatom silica. The isotopic effects of opal-CT are not as clearly understood and more difficult to physically separate from the primary diatom silica. In order to better understand the isotope variations in the AND-1B diatoms, we also evaluated silicon and oxygen isotope fractionation during the transition from opal-A to opal-CT in a controlled laboratory experiment. Opal-A from cultured marine diatoms (Thalassiosira weissflogii) was subjected to elevated temperatures (150°C) in acid digestion vessels for 4 weeks to initiate opal-CT precipitation. Quantifying the effects of opal-CT formation on δ18O and δ30Si variations in biogenic silica improves our understanding of the use of diatom silica isotope values a paleoenvironmental proxy throughout the Cenozoic.

The cascade construction of artificial ponds as a tool for urban stream restoration - The use of benthic diatoms to assess the effects of restoration practices.

PubMed

Żelazna-Wieczorek, Joanna; Nowicka-Krawczyk, Paulina

2015-12-15

A series of cascade artificial ponds were constructed to improve the ecological status of the stream. To evaluate the effects of restoration practices, a bioassessment, based on phytobenthic algae - the diatoms, was made. Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA) of diatom assemblages allowed for evaluating the influence of a series of cascade artificial ponds on stream integrity. To reveal which environmental factors had the greatest influence on shaping diatom assemblages, the BIO-ENV procedure was used, and in order to examine whether these factors had equal influence on diatoms along the stream, Redundancy Analysis (RDA) was used. The analysis of diatom assemblages allowed for the calculation of the diatom indices in order to assess the water quality and the ecological status of the stream. Artificial ponds constructed on the stream had significant effects on the integrity of the stream ecosystem. Diatom assemblages characteristic of stream habitats were disrupted by the species from ponds. HCA and PCA revealed that the stream was clearly divided into three sections: ponds, stream parts under the influence of ponds, and stream parts isolated from ponds. The ponds thus altered stream environmental conditions. Benthic diatom assemblages were affected by a combination of four environmental factors: the concentration of ammonium ions, dissolved oxygen, conductivity, and the amount of total suspended material in the water. These factors, together with water pH, had a diverse influence on diatom assemblages alongside the stream, which was caused by a series of cascade ponds. In theory, this restoration practice should restore the stream close to its natural state, but bioassessment of the stream ecosystem based on diatoms revealed that there was no improvement of the ecological status alongside the stream. The construction of artificial ponds disrupted stream continuity and altered the character of the stream ecosystem. Copyright © 2015 Elsevier B.V. All rights reserved.

A caveat regarding diatom-inferred nitrogen concentrations in oligotrophic lakes

USGS Publications Warehouse

Arnett, Heather A.; Saros, Jasmine E.; Mast, M. Alisa

2012-01-01

Atmospheric deposition of reactive nitrogen (Nr) has enriched oligotrophic lakes with nitrogen (N) in many regions of the world and elicited dramatic changes in diatom community structure. The lakewater concentrations of nitrate that cause these community changes remain unclear, raising interest in the development of diatom-based transfer functions to infer nitrate. We developed a diatom calibration set using surface sediment samples from 46 high-elevation lakes across the Rocky Mountains of the western US, a region spanning an N deposition gradient from very low to moderate levels (<1 to 3.2 kg Nr ha−1 year−1 in wet deposition). Out of the fourteen measured environmental variables for these 46 lakes, ordination analysis identified that nitrate, specific conductance, total phosphorus, and hypolimnetic water temperature were related to diatom distributions. A transfer function was developed for nitrate and applied to a sedimentary diatom profile from Heart Lake in the central Rockies. The model coefficient of determination (bootstrapping validation) of 0.61 suggested potential for diatom-inferred reconstructions of lakewater nitrate concentrations over time, but a comparison of observed versus diatom-inferred nitrate values revealed the poor performance of this model at low nitrate concentrations. Resource physiology experiments revealed that nitrogen requirements of two key taxa were opposite to nitrate optima defined in the transfer function. Our data set reveals two underlying ecological constraints that impede the development of nitrate transfer functions in oligotrophic lakes: (1) even in lakes with nitrate concentrations below quantification (<1 μg L−1), diatom assemblages were already dominated by species indicative of moderate N enrichment; (2) N-limited oligotrophic lakes switch to P limitation after receiving only modest inputs of reactive N, shifting the controls on diatom species changes along the length of the nitrate gradient. These constraints suggest that quantitative inferences of nitrate from diatom assemblages will likely require experimental approaches.

Diatoms as a paleoproductivity proxy in the NW Iberian coastal upwelling system (NE Atlantic)

NASA Astrophysics Data System (ADS)

Zúñiga, Diana; Santos, Celia; Froján, María; Salgueiro, Emilia; Rufino, Marta M.; De la Granda, Francisco; Figueiras, Francisco G.; Castro, Carmen G.; Abrantes, Fátima

2017-03-01

The objective of the current work is to improve our understanding of how water column diatom's abundance and assemblage composition is seasonally transferred from the photic zone to seafloor sediments. To address this, we used a dataset derived from water column, sediment trap and surface sediment samples recovered in the NW Iberian coastal upwelling system. Diatom fluxes (2.2 (±5.6) 106 valves m-2 d-1) represented the majority of the siliceous microorganisms sinking out from the photic zone during all studied years and showed seasonal variability. Contrasting results between water column and sediment trap diatom abundances were found during downwelling periods, as shown by the unexpectedly high diatom export signals when diatom-derived primary production achieved their minimum levels. They were principally related to surface sediment remobilization and intense Minho and Douro river discharge that constitute an additional source of particulate matter to the inner continental shelf. In fact, contributions of allochthonous particles to the sinking material were confirmed by the significant increase of both benthic and freshwater diatoms in the sediment trap assemblage. In contrast, we found that most of the living diatom species blooming during highly productive upwelling periods were dissolved during sinking, and only those resistant to dissolution and the Chaetoceros and Leptocylindrus spp. resting spores were susceptible to being exported and buried. Furthermore, Chaetoceros spp. dominate during spring-early summer, when persistent northerly winds lead to the upwelling of nutrient-rich waters on the shelf, while Leptocylindrus spp. appear associated with late-summer upwelling relaxation, characterized by water column stratification and nutrient depletion. These findings evidence that the contributions of these diatom genera to the sediment's total marine diatom assemblage should allow for the reconstruction of different past upwelling regimes.

Diatoms as an indicator for tile drainage flow in a German lowland catchment.

PubMed

Wu, Naicheng; Faber, Claas; Ulrich, Uta; Fohrer, Nicola

2018-01-01

The separation of runoff components within a model simulation is of great importance for a successful implementation of management measures. Diatoms could be a promising indicator for tile drainage flow due to their diverse preferences to different aquatic habitats. In this study, we collected diatom samples of 9 sites (4 tile drainage, TD, and 5 river sites, Ri) in a German lowland catchment at a weekly or biweekly time step from March to July 2013 with the aim of testing the suitability of diatoms for tile drainage flow, which is typical for lowland catchment. Planothidium lanceolatum , Ulnaria biceps , and Navicula gregaria dominated in TD sites with relative abundances of 22.2, 21.5, and 10.9%, respectively. For Ri sites, the most abundant species was Navicula lanceolata (20.5%), followed by Ulnaria biceps (12.9%), Cyclotella meneghiniana (9.5%), and Planothidium lanceolatum (9.3%). Compared with Ri sites, TD had a lower diatom density, biomass, species richness, and percentage of Aquatic/Riparian diatoms (AqRi%). However, the proportion of Riparian diatoms (RiZo%) increased at TD. Indicator value method (IndVal) revealed that the two groups (Ri and TD) were characterized by different indicator species. Fifteen taxa, including Cocconeis placentula , Cyclotella meneghiniana , N. lanceolata , and U. biceps , were significant indicators for Ri sites. Planothidium lanceolatum , Achnanthidium minutissimum , and Navicula gregaria were significant indicators for TD sites. A pronounced variation was found in the species lists of diatom community between Ri and TD water body types associated with different indicator species. With respect to hydrograph separation, these findings highlight the suitability of diatoms as an indicator for tile drainage flow. However, spatial and temporal variations of diatoms should be considered in future surveys.

Diatom genomics: genetic acquisitions and mergers.

PubMed

Nisbet, R Ellen R; Kilian, Oliver; McFadden, Geoffrey I

2004-12-29

Diatom algae arose by two-step endosymbiosis. The complete genome of the diatom Thalassiosira pseudonana has now been sequenced, allowing us to reconstruct the remarkable intracellular gene transfers that occurred during this convoluted cellular evolution.

Acoustic propagation operators for pressure waves on an arbitrarily curved surface in a homogeneous medium

NASA Astrophysics Data System (ADS)

Sun, Yimin; Verschuur, Eric; van Borselen, Roald

2018-03-01

The Rayleigh integral solution of the acoustic Helmholtz equation in a homogeneous medium can only be applied when the integral surface is a planar surface, while in reality almost all surfaces where pressure waves are measured exhibit some curvature. In this paper we derive a theoretically rigorous way of building propagation operators for pressure waves on an arbitrarily curved surface. Our theory is still based upon the Rayleigh integral, but it resorts to matrix inversion to overcome the limitations faced by the Rayleigh integral. Three examples are used to demonstrate the correctness of our theory - propagation of pressure waves acquired on an arbitrarily curved surface to a planar surface, on an arbitrarily curved surface to another arbitrarily curved surface, and on a spherical cap to a planar surface, and results agree well with the analytical solutions. The generalization of our method for particle velocities and the calculation cost of our method are also discussed.

Arbitrarily small amounts of correlation for arbitrarily varying quantum channels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boche, H., E-mail: boche@tum.de, E-mail: janis.noetzel@tum.de; Nötzel, J., E-mail: boche@tum.de, E-mail: janis.noetzel@tum.de

2013-11-15

As our main result show that in order to achieve the randomness assisted message and entanglement transmission capacities of a finite arbitrarily varying quantum channel it is not necessary that sender and receiver share (asymptotically perfect) common randomness. Rather, it is sufficient that they each have access to an unlimited amount of uses of one part of a correlated bipartite source. This access might be restricted to an arbitrary small (nonzero) fraction per channel use, without changing the main result. We investigate the notion of common randomness. It turns out that this is a very costly resource – generically, itmore » cannot be obtained just by local processing of a bipartite source. This result underlines the importance of our main result. Also, the asymptotic equivalence of the maximal- and average error criterion for classical message transmission over finite arbitrarily varying quantum channels is proven. At last, we prove a simplified symmetrizability condition for finite arbitrarily varying quantum channels.« less

Brownian motion of arbitrarily shaped particles in two dimensions.

PubMed

Chakrabarty, Ayan; Konya, Andrew; Wang, Feng; Selinger, Jonathan V; Sun, Kai; Wei, Qi-Huo

2014-11-25

We implement microfabricated boomerang particles with unequal arm lengths as a model for nonsymmetric particles and study their Brownian motion in a quasi-two-dimensional geometry by using high-precision single-particle motion tracking. We show that because of the coupling between translation and rotation, the mean squared displacements of a single asymmetric boomerang particle exhibit a nonlinear crossover from short-time faster to long-time slower diffusion, and the mean displacements for fixed initial orientation are nonzero and saturate out at long times. The measured anisotropic diffusion coefficients versus the tracking point position indicate that there exists one unique point, i.e., the center of hydrodynamic stress (CoH), at which all coupled diffusion coefficients vanish. This implies that in contrast to motion in three dimensions where the CoH exists only for high-symmetry particles, the CoH always exists for Brownian motion in two dimensions. We develop an analytical model based on Langevin theory to explain the experimental results and show that among the six anisotropic diffusion coefficients only five are independent because the translation-translation coupling originates from the translation-rotation coupling. Finally, we classify the behavior of two-dimensional Brownian motion of arbitrarily shaped particles into four groups based on the particle shape symmetry group and discussed potential applications of the CoH in simplifying understanding of the circular motions of microswimmers.

Iron Storage Capacity and its Ecological Role within Phylogenetically Distinct Marine Diatoms

NASA Astrophysics Data System (ADS)

Cohen, N.; Jacquot, J. E.; Stemple, B.; Sunda, W. G.; Twining, B. S.; Marchetti, A.

2016-02-01

Natural and artificial iron fertilization occurring in iron-limited regions of the ocean often results in large blooms of pennate diatoms. The ability of these pennate diatoms to quickly respond to bioavailable iron and proliferate has been attributed in part to their use of the iron storage protein ferritin. Recent concerted efforts to sequence the transcriptomes of eukaryotic protists have made it apparent that some, but not all, centric diatoms also possess a ferritin gene homolog. Using a combination of physiological and molecular biological techniques, we determined the cellular iron quotas and associated ferritin gene expression within both ferritin-containing and non-containing centric and pennate diatoms grown under a range of iron concentrations. Our results show that under steady-state conditions there are no clear differences between the maximum iron cellular quotas of ferritin-containing versus non-ferritin containing centric and pennate diatoms. However, based on differences in gene expression patterns, ferritin appears to play fundamentally different functional roles between centric and pennate diatoms. We propose the success of oceanic pennate diatoms such as Pseudo-nitzschia following iron addition is not only a function of achieving a high iron storage capacity, but also due to their unique ability to drastically reduce intracellular iron requirements while still maintaining rapid growth rates, and depends on iron bioavailability in the environment.

Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.

PubMed

Broman, Elias; Sachpazidou, Varvara; Dopson, Mark; Hylander, Samuel

2017-10-11

An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats. © 2017 The Author(s).

Codon adaptation and synonymous substitution rate in diatom plastid genes.

PubMed

Morton, Brian R; Sorhannus, Ulf; Fox, Martin

2002-07-01

Diatom plastid genes are examined with respect to codon adaptation and rates of silent substitution (Ks). It is shown that diatom genes follow the same pattern of codon usage as other plastid genes studied previously. Highly expressed diatom genes display codon adaptation, or a bias toward specific major codons, and these major codons are the same as those in red algae, green algae, and land plants. It is also found that there is a strong correlation between Ks and variation in codon adaptation across diatom genes, providing the first evidence for such a relationship in the algae. It is argued that this finding supports the notion that the correlation arises from selective constraints, not from variation in mutation rate among genes. Finally, the diatom genes are examined with respect to variation in Ks among different synonymous groups. Diatom genes with strong codon adaptation do not show the same variation in synonymous substitution rate among codon groups as the flowering plant psbA gene which, previous studies have shown, has strong codon adaptation but unusually high rates of silent change in certain synonymous groups. The lack of a similar finding in diatoms supports the suggestion that the feature is unique to the flowering plant psbA due to recent relaxations in selective pressure in that lineage.

A diatom record of climate and hydrology for the past 200 KA from Owens Lake, California with comparison to other Breat Basin records

USGS Publications Warehouse

Bradbury, J.P.

1997-01-01

Diatoms from lake sediments beneath Owens Lake playa, Inyo County, California, document a nearly continuous paleolimnological record of climate and hydrologic change since the penultimate glacial-interglacial cycle based on a chronology established by radiocarbon, tephrochronology, and paleomagnetic control. Freshwater planktic diatoms (especially species of Stephanodiscus), plagioclase feldspar-rich sediments with high magnetic susceptibility, and Juniperus-type pollen characterized the penultimate glaciation at Owens Lake. Saline diatoms dominated in the following interglacial period, and there are several episodes during which freshwater planktic diatoms became abundant between 100 and 50 ka that may represent interstadial climatic conditions. Saline diatoms fell to low values after 50 ka, but warm-season Aulacoseira species indicate episodes of significant summer precipitation in the hydrologic balance of Owens Lake prior to the last glacial maximum. By 25 ka, glacial environments were again characterized by abundant Juniperus, plagioclase feldspar, and Stephanodiscus species. Generally and Holocene climates were recorded in Owens Lake by short-term fluctuations of saline and freshwater diatoms, desiccation, and oolitic sediments barren of diatoms. Comparison to paleoclimate records both north and south of Owens Lake suggest a southerly displacement of storm tracks originating from the Aleutian Low during glacial episodes.

Indicators: Sediment Diatoms

EPA Pesticide Factsheets

Diatoms are a type of algae that are typically abundant in marine and freshwater ecosystems. They have inorganic cell walls made up of silica (glass). Diatoms most commonly grow suspended in water, although they can also attach to substrates.

Induction of Protease Release of the Resistant Diatom Chaetoceros didymus in Response to Lytic Enzymes from an Algicidal Bacterium

PubMed Central

Paul, Carsten; Pohnert, Georg

2013-01-01

Marine lytic bacteria can have a substantial effect on phytoplankton and are even capable to terminate blooms of microalgae. The bacterium Kordia algicida was reported to lyse cells of the diatom Skeletonema costatum and several other diatoms by a quorum sensing controlled excretion of proteases. However the diatom Chaetoceros didymus is fully resistant against the bacterial enzymes. We show that the growth curve of this diatom is essentially unaffected by addition of bacterial filtrates that are active against other diatoms. By monitoring proteases from the medium using zymography and fluorescence based activity assays we demonstrate that C. didymus responds to the presence of the lytic bacteria with the induced production of algal proteases. These proteases exhibit a substantially increased activity compared to the bacterial counterparts. The induction is also triggered by signals in the supernatant of a K. algicida culture. Size fractionation shows that only the >30 kD fraction of the bacterial exudates acts as an inducing cue. Implications for a potential induced defense of the diatom C. didymus are discussed. PMID:23469204

Interactive effects of nitrogen and light on growth rates and RUBISCO content of small and large centric diatoms.

PubMed

Li, Gang; Campbell, Douglas A

2017-01-01

Among marine phytoplankton groups, diatoms span the widest range of cell size, with resulting effects upon their nitrogen uptake, photosynthesis and growth responses to light. We grew two strains of marine centric diatoms differing by ~4 orders of magnitude in cell biovolume in high (enriched artificial seawater with ~500 µmol L -1  µmol L -1  NO 3 - ) and lower-nitrogen (enriched artificial seawater with <10 µmol L -1  NO 3 - ) media, across a range of growth light levels. Nitrogen and total protein per cell decreased with increasing growth light in both species when grown under the lower-nitrogen media. Cells growing under lower-nitrogen media increased their cellular allocation to RUBISCO and their rate of electron transport away from PSII, for the smaller diatom under low growth light and for the larger diatom across the range of growth lights. The smaller coastal diatom Thalassiosira pseudonana is able to exploit high nitrogen in growth media by up-regulating growth rate, but the same high-nitrogen growth media inhibits growth of the larger diatom species.

Update of the Diatom EST Database: a new tool for digital transcriptomics

PubMed Central

Maheswari, Uma; Mock, Thomas; Armbrust, E. Virginia; Bowler, Chris

2009-01-01

The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130 000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77 000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3. PMID:19029140

Marennine, Promising Blue Pigments from a Widespread Haslea Diatom Species Complex

PubMed Central

Gastineau, Romain; Turcotte, François; Pouvreau, Jean-Bernard; Morançais, Michèle; Fleurence, Joël; Windarto, Eko; Semba Prasetiya, Fiddy; Arsad, Sulastri; Jaouen, Pascal; Babin, Mathieu; Coiffard, Laurence; Couteau, Céline; Bardeau, Jean-François; Jacquette, Boris; Leignel, Vincent; Hardivillier, Yann; Marcotte, Isabelle; Bourgougnon, Nathalie; Tremblay, Réjean; Deschênes, Jean-Sébastien; Badawy, Hope; Pasetto, Pamela; Davidovich, Nikolai; Hansen, Gert; Dittmer, Jens; Mouget, Jean-Luc

2014-01-01

In diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. The marine pennate diatom Haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. This pigment, responsible for the greening of oysters in western France, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. A method to extract and purify marennine has been developed, but its chemical structure could hitherto not be resolved. For decades, H. ostrearia was the only organism known to produce marennine, and can be found worldwide. Our knowledge about H. ostrearia-like diatom biodiversity has recently been extended with the discovery of several new species of blue diatoms, the recently described H. karadagensis, H. silbo sp. inedit. and H. provincialis sp. inedit. These blue diatoms produce different marennine-like pigments, which belong to the same chemical family and present similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms thus present a commercial potential for aquaculture, cosmetics, food and health industries. PMID:24879542

Structure-based optics of centric diatom frustules: modulation of the in vivo light field for efficient diatom photosynthesis.

PubMed

Goessling, Johannes W; Su, Yanyan; Cartaxana, Paulo; Maibohm, Christian; Rickelt, Lars F; Trampe, Erik C L; Walby, Sandra L; Wangpraseurt, Daniel; Wu, Xia; Ellegaard, Marianne; Kühl, Michael

2018-07-01

The optical properties of diatom silicate frustules inspire photonics and nanotechnology research. Whether light interaction with the nano-structure of the frustule also affects diatom photosynthesis has remained unclear due to lack of information on frustule optical properties under more natural conditions. Here we demonstrate that the optical properties of the frustule valves in water affect light harvesting and photosynthesis in live cells of centric diatoms (Coscinodiscus granii). Microscale cellular mapping of photosynthesis around localized spot illumination demonstrated optical coupling of chloroplasts to the valve wall. Photonic structures of the three-layered C. granii valve facilitated light redistribution and efficient photosynthesis in cell regions distant from the directly illuminated area. The different porous structure of the two sides of the valve exhibited photon trapping and forward scattering of blue light enhancing photosynthetic active radiation inside the cell. Photonic structures of diatom frustules thus alter the cellular light field with implications on diatom photobiology. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Morphological and transcriptomic evidence for ammonium induction of sexual reproduction in Thalassiosira pseudonana and other centric diatoms

PubMed Central

Moore, Eric R.; Bullington, Briana S.; Weisberg, Alexandra J.; Jiang, Yuan; Chang, Jeff

2017-01-01

The reproductive strategy of diatoms includes asexual and sexual phases, but in many species, including the model centric diatom Thalassiosira pseudonana, sexual reproduction has never been observed. Furthermore, the environmental factors that trigger sexual reproduction in diatoms are not understood. Although genome sequences of a few diatoms are available, little is known about the molecular basis for sexual reproduction. Here we show that ammonium reliably induces the key sexual morphologies, including oogonia, auxospores, and spermatogonia, in two strains of T. pseudonana, T. weissflogii, and Cyclotella cryptica. RNA sequencing revealed 1,274 genes whose expression patterns changed when T. pseudonana was induced into sexual reproduction by ammonium. Some of the induced genes are linked to meiosis or encode flagellar structures of heterokont and cryptophyte algae. The identification of ammonium as an environmental trigger suggests an unexpected link between diatom bloom dynamics and strategies for enhancing population genetic diversity. PMID:28686696

Data report: Mid-Pliocene diatom assemblages at sites 1016, 1021, and 1022

USGS Publications Warehouse

Barron, John A.; Nessler, Susan; Miller, Christine M.; Peters, Lori L.

2000-01-01

Diatom assemblages from the middle part of the Pliocene (3.2-2.5 Ma) were investigated from Ocean Drilling Program Sites 1016, 1021, and 1022 in an effort to infer paleotemperature fluctuations off California.Diatoms are very sparse in virtually all of the samples that were examined from Sites 1016 and 1021. This is presumably because these sites were seaward (west) of the coastal zone of diatom productivity during the middle part of the Pliocene.Diatoms are relatively common in the vast majority of samples that were examined from Hole 1022A. Diatom assemblages are dominated by Chaetoceros spores (a coastal upwelling component), the cold-water (subarctic) taxa Neodenticula kamtschatica and its descendant Neodenticula koizumii, and Thalassionema nitzschioides, a temperate taxon that is typically found at the seaward edge of coastal upwelling zones. Paleotemperature interpretations, however, are not possible at this time because of the scarcity of comparative modern core-top data.

Extraction of diatoms from (cotton) clothing for forensic comparisons.

PubMed

Uitdehaag, Stefan; Dragutinovic, Aleksandar; Kuiper, Irene

2010-07-15

Diatoms in clothing can be used to determine contact with surface water and contact with a specific water source, which can help link suspects to crime scenes. However, for the study of diatoms it is imperative that they are first extracted from the clothing under investigation. In this study we tested three methods for extracting diatoms from cotton clothing: rinsing with water (RW), rinsing with ethanol (RE) and the dissolution of cotton with nitric and sulphuric acid (DI). The DI method produced the highest average yield and can be used to determine contact with water. The RE method extracted reproducible numbers of diatoms from two different T-shirts and the resulting species compositions were similar to their relevant reference water samples. Therefore, we present rinsing with ethanol as an effective extraction method for the qualitative and quantitative analysis of diatoms in (cotton) clothing. (c) 2010 Elsevier Ireland Ltd. All rights reserved.

The influence of reduced light intensity on the response of benthic diatoms to herbicide exposure.

PubMed

Wood, Rebecca J; Mitrovic, Simon M; Lim, Richard P; Kefford, Ben J

2016-09-01

Herbicide pollution events in aquatic ecosystems often coincide with increased turbidity and reduced light intensity. It is therefore important to determine whether reduced light intensity can influence herbicide toxicity, especially to primary producers such as benthic diatoms. Benthic diatoms collected from 4 rivers were exposed to herbicides in 48 h rapid toxicity tests under high light (100 µmol m(-2)  s(-1) ) and low light (20 µmol m(-2)  s(-1) ) intensities. The effects of 2 herbicides (atrazine and glyphosate) were assessed on 26 freshwater benthic diatom taxa. There was no significant interaction of light and herbicide effects at the community level or on the majority (22 of 26) of benthic diatom taxa. This indicates that low light levels will likely have only a minor influence on the response of benthic diatoms to herbicides. Environ Toxicol Chem 2016;35:2252-2260. © 2016 SETAC. © 2016 SETAC.

Isolation and biochemical characterization of underwater adhesives from diatoms.

PubMed

Poulsen, Nicole; Kröger, Nils; Harrington, Matthew J; Brunner, Eike; Paasch, Silvia; Buhmann, Matthias T

2014-01-01

Many aquatic organisms are able to colonize surfaces through the secretion of underwater adhesives. Diatoms are unicellular algae that have the capability to colonize any natural and man-made submerged surfaces. There is great technological interest in both mimicking and preventing diatom adhesion, yet the biomolecules responsible have so far remained unidentified. A new method for the isolation of diatom adhesive material is described and its amino acid and carbohydrate composition determined. The adhesive materials from two model diatoms show differences in their amino acid and carbohydrate compositions, but also share characteristic features including a high content of uronic acids, the predominance of hydrophilic amino acid residues, and the presence of 3,4-dihydroxyproline, an extremely rare amino acid. Proteins containing dihydroxyphenylalanine, which mediate underwater adhesion of mussels, are absent. The data on the composition of diatom adhesives are consistent with an adhesion mechanism based on complex coacervation of polyelectrolyte-like biomolecules.

Ubiquitous marine bacterium inhibits diatom cell division.

PubMed

van Tol, Helena M; Amin, Shady A; Armbrust, E Virginia

2017-01-01

Intricate relationships between microorganisms structure the exchange of molecules between taxa, driving their physiology and evolution. On a global scale, this molecular trade is an integral component of biogeochemical cycling. As important microorganisms in the world's oceans, diatoms and bacteria have a large impact on marine biogeochemistry. Here, we describe antagonistic effects of the globally distributed flavobacterium Croceibacter atlanticus on a phylogenetically diverse group of diatoms. We used the model diatom Thalassiosira pseudonana to study the antagonistic impact in more detail. In co-culture, C. atlanticus attaches to T. pseudonana and inhibits cell division, inducing diatom cells to become larger and increase in chlorophyll a fluorescence. These changes could be explained by an absence of cytokinesis that causes individual T. pseudonana cells to elongate, accumulate more plastids and become polyploid. These morphological changes could benefit C. atlanticus by augmenting the colonizable surface area of the diatom, its photosynthetic capabilities and possibly its metabolic secretions.

A role for diatom-like silicon transporters in calcifying coccolithophores

PubMed Central

Durak, Grażyna M.; Taylor, Alison R.; Walker, Charlotte E.; Probert, Ian; de Vargas, Colomban; Audic, Stephane; Schroeder, Declan; Brownlee, Colin; Wheeler, Glen L.

2016-01-01

Biomineralization by marine phytoplankton, such as the silicifying diatoms and calcifying coccolithophores, plays an important role in carbon and nutrient cycling in the oceans. Silicification and calcification are distinct cellular processes with no known common mechanisms. It is thought that coccolithophores are able to outcompete diatoms in Si-depleted waters, which can contribute to the formation of coccolithophore blooms. Here we show that an expanded family of diatom-like silicon transporters (SITs) are present in both silicifying and calcifying haptophyte phytoplankton, including some globally important coccolithophores. Si is required for calcification in these coccolithophores, indicating that Si uptake contributes to the very different forms of biomineralization in diatoms and coccolithophores. Significantly, SITs and the requirement for Si are absent from highly abundant bloom-forming coccolithophores, such as Emiliania huxleyi. These very different requirements for Si in coccolithophores are likely to have major influence on their competitive interactions with diatoms and other siliceous phytoplankton. PMID:26842659

Morphological and transcriptomic evidence for ammonium induction of sexual reproduction in Thalassiosira pseudonana and other centric diatoms.

PubMed

Moore, Eric R; Bullington, Briana S; Weisberg, Alexandra J; Jiang, Yuan; Chang, Jeff; Halsey, Kimberly H

2017-01-01

The reproductive strategy of diatoms includes asexual and sexual phases, but in many species, including the model centric diatom Thalassiosira pseudonana, sexual reproduction has never been observed. Furthermore, the environmental factors that trigger sexual reproduction in diatoms are not understood. Although genome sequences of a few diatoms are available, little is known about the molecular basis for sexual reproduction. Here we show that ammonium reliably induces the key sexual morphologies, including oogonia, auxospores, and spermatogonia, in two strains of T. pseudonana, T. weissflogii, and Cyclotella cryptica. RNA sequencing revealed 1,274 genes whose expression patterns changed when T. pseudonana was induced into sexual reproduction by ammonium. Some of the induced genes are linked to meiosis or encode flagellar structures of heterokont and cryptophyte algae. The identification of ammonium as an environmental trigger suggests an unexpected link between diatom bloom dynamics and strategies for enhancing population genetic diversity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Armbrust, E V; Berges, J A; Bowler, C

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in themore » marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different evolutionary history from the higher plants that dominate photosynthesis on land. Higher plants and green, red and glaucophyte algae are derived from a primary endosymbiotic event in which a non-photosynthetic eukaryote acquired a chloroplast by engulfing (or being invaded by) a prokaryotic cyanobacterium. In contrast, dominant bloom-forming eukaryotic phytoplankton in the ocean, such as diatoms and haptophytes, were derived by secondary endosymbiosis whereby a non-photosynthetic eukaryote acquired a chloroplast by engulfing a photosynthetic eukaryote, probably a red algal endosymbiont (Fig. 1). Each endosymbiotic event led to new combinations of genes derived from the hosts and endosymbionts (7). Prior to this project, relatively few diatom genes had been sequenced, few chromosome numbers were known, and genetic maps did not exist (8). The ecological and evolutionary importance of diatoms motivated our sequencing and analysis of the nuclear, plastid, and mitochondrial genomes of the marine centric diatom Thalassiosira pseudonana.« less

Solute rotational dynamics at the water liquid/vapor interface.

PubMed

Benjamin, Ilan

2007-11-28

The rotational dynamics of a number of diatomic molecules adsorbed at different locations at the interface between water and its own vapors are studied using classical molecular dynamics computer simulations. Both equilibrium orientational and energy correlations and nonequilibrium orientational and energy relaxation correlations are calculated. By varying the dipole moment of the molecule and its location, and by comparing the results with those in bulk water, the effects of dielectric and mechanical frictions on reorientation dynamics and on rotational energy relaxation can be studied. It is shown that for nonpolar and weekly polar solutes, the equilibrium orientational relaxation is much slower in the bulk than at the interface. As the solute becomes more polar, the rotation slows down and the surface and bulk dynamics become similar. The energy relaxation (both equilibrium and nonequilibrium) has the opposite trend with the solute dipole (larger dipoles relax faster), but here again the bulk and surface results converge as the solute dipole is increased. It is shown that these behaviors correlate with the peak value of the solvent-solute radial distribution function, which demonstrates the importance of the first hydration shell structure in determining the rotational dynamics and dependence of these dynamics on the solute dipole and location.

Homeotropic alignment and Förster resonance energy transfer: The way to a brighter luminescent solar concentrator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tummeltshammer, Clemens; Taylor, Alaric; Kenyon, Anthony J.

2014-11-07

We investigate homeotropically aligned fluorophores and Förster resonance energy transfer (FRET) for luminescent solar concentrators using Monte-Carlo ray tracing. The homeotropic alignment strongly improves the trapping efficiency, while FRET circumvents the low absorption at homeotropic alignment by separating the absorption and emission processes. We predict that this design doped with two organic dye molecules can yield a 82.9% optical efficiency improvement compared to a single, arbitrarily oriented dye molecule. We also show that quantum dots are prime candidates for absorption/donor fluorophores due to their wide absorption band. The potentially strong re-absorption and low quantum yield of quantum dots is notmore » a hindrance for this design.« less

Modeling the electrophoretic separation of short biological molecules in nanofluidic devices

NASA Astrophysics Data System (ADS)

Fayad, Ghassan; Hadjiconstantinou, Nicolas

2010-11-01

Via comparisons with Brownian Dynamics simulations of the worm-like-chain and rigid-rod models, and the experimental results of Fu et al. [Phys. Rev. Lett., 97, 018103 (2006)], we demonstrate that, for the purposes of low-to-medium field electrophoretic separation in periodic nanofilter arrays, sufficiently short biomolecules can be modeled as point particles, with their orientational degrees of freedom accounted for using partition coefficients. This observation is used in the present work to build a particularly simple and efficient Brownian Dynamics simulation method. Particular attention is paid to the model's ability to quantitatively capture experimental results using realistic values of all physical parameters. A variance-reduction method is developed for efficiently simulating arbitrarily small forcing electric fields.

LEGO: A modular accelerator design code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Y.; Donald, M.; Irwin, J.

1997-08-01

An object-oriented accelerator design code has been designed and implemented in a simple and modular fashion. It contains all major features of its predecessors: TRACY and DESPOT. All physics of single-particle dynamics is implemented based on the Hamiltonian in the local frame of the component. Components can be moved arbitrarily in the three dimensional space. Several symplectic integrators are used to approximate the integration of the Hamiltonian. A differential algebra class is introduced to extract a Taylor map up to arbitrary order. Analysis of optics is done in the same way both for the linear and nonlinear case. Currently, themore » code is used to design and simulate the lattices of the PEP-II. It will also be used for the commissioning.« less

Widefield and total internal reflection fluorescent structured illumination microscopy with scanning galvo mirrors

NASA Astrophysics Data System (ADS)

Chen, Youhua; Cao, Ruizhi; Liu, Wenjie; Zhu, Dazhao; Zhang, Zhiming; Kuang, Cuifang; Liu, Xu

2018-04-01

We present an alternative approach to realize structured illumination microscopy (SIM), which is capable for live cell imaging. The prototype utilizes two sets of scanning galvo mirrors, a polarization converter and a piezo-platform to generate a fast shifted, s-polarization interfered and periodic variable illumination patterns. By changing the angle of the scanning galvanometer, we can change the position of the spots at the pupil plane of the objective lens arbitrarily, making it easy to switch between widefield and total internal reflection fluorescent-SIM mode and adapting the penetration depth in the sample. Also, a twofold resolution improvement is achieved in our experiments. The prototype offers more flexibility of pattern period and illumination orientation changing than previous systems.

Production of silver nanoparticles by the diatom Phaeodactylum tricornutum

NASA Astrophysics Data System (ADS)

Wishkerman, Asher; Arad (Malis), Shoshana

2017-05-01

Diatoms (Bacillariophyceae) are the most species-rich group of algae, they are single-celled characterized by a silicified cell wall called a frustule. Diatoms are diverse in shape with many distinct features like raphe and fultoportulae. The diatom cell wall morphology and its hierarchy structure make it a unique unicellular organism for nanotechnology research and applications. Diatom cells are a promising system for green synthesis of nanomaterials like metallic nanoparticles (NPs), nanostructured polymers and other nanomaterials. The production of NPs is achieved today by using methods like attrition or pyrolysis. The cost and the toxic substances often used in these common methods of NPs synthesis limit their applications. Therefore, NPs biosynthesis by diatom cultures, which can be done at ambient CO2 concentrations, temperature and pressure, offers a sustainable alternative solution. In this work, we examined the formation of silver NPs (AgNPs) by the diatom Phaeodactylum tricornutum cultivated at 25°C for a period of 8 days. Using this approach, diatom cultures were either grown throughout the duration of the experiment in an artificial seawater (ASW)-f/2 medium enriched with 1 ppm Ag+ or grown in an ASW-f/2 medium where similar silver ion concentrations were added on experimental day 4. We found that 1 ppm Ag+ reduces the P. tricornutum growth by up to 50% as compared with the control. Moreover, scanning electron microscopy (SEM) in combination with Energy-Dispersive X-ray (EDX) showed the presence of AgNPs nanoparticles with different sizes and chemical composition associated with the diatom frustules and extracellular polymeric substances.

A kinematic analysis of the Space Station remote manipulator system (SSRMS)

NASA Technical Reports Server (NTRS)

Crane, Carl D., III; Duffy, Joseph; Carnahan, Tim

1991-01-01

An efficient reverse analysis of three 6-degree-of-freedom (dof) subchains of the 7-dof SSRMS is presented. The first subchain is formed by locking the seventh joint. The second subchain is formed by locking the second joint, while the third subchain is formed by locking the first joint (the grounded joint is counted as the first joint in the chain). There are a maximum of eight different arm configurations in each of the three subchains, and these were determined by employing a computer-efficient algorithm, which required the rooting of only at most quadratic polynomials. The algorithms were implemented, and the SSRMS was employed in an animated environment to perform and practice a number of useful tasks for Space Station servicing. The locking of the second joint has the advantage in that an operator can choose the orientation of the plane that contains the two longest links so as to avoid collisions with obstacles. However, it has the disadvantage that when the second joint angle equals 0 deg or 180 deg, the manipulator is in a singularity configuration. This plane can also be oriented by specifying the first joint angle, so that the plane can be oriented arbitrarily and, in this, the singularity is avoided.

Analysis of the substrate influence on the ordering of epitaxial molecular layers: The special case of point-on-line coincidence

NASA Astrophysics Data System (ADS)

Mannsfeld, S. C.; Fritz, T.

2004-02-01

The physical structure of organic-inorganic heteroepitaxial thin films is usually governed by a fine balance between weak molecule-molecule interactions and a weakly laterally varying molecule-substrate interaction potential. Therefore, in order to investigate the energetics of such a layer system one has to consider large molecular domains. So far, layer potential calculations for large domains of organic thin films on crystalline substrates were difficult to perform concerning the computational effort which stems from the vast number of atoms which have to be included. Here, we present a technique which enables the calculation of the molecule-substrate interaction potential for large molecular domains by utilizing potential energy grid files. This technique allows the investigation of the substrate influence in systems prepared by organic molecular beam epitaxy (OMBE), like 3,4,9,10-perylenetetracarboxylicdianhydride on highly oriented pyrolytic graphite. For this system the so-called point-on-line coincidence was proposed, a growth mode which has been controversially discussed in literature. Furthermore, we are able to provide evidence for a general energetic advantage of such point-on-line coincident domain orientations over arbitrarily oriented domains which substantiates that energetically favorable lattice structures in OMBE systems are not restricted to commensurate unit cells or coincident super cells.

Earth Reflected Solar Radiation Incident upon an Arbitrarily Oriented Spinning Flat Plate

NASA Technical Reports Server (NTRS)

Cunningham, Fred G.

1963-01-01

A general derivation is given for the earth reflected solar radiation input to a flat plate--a solar cell paddle, for example--which is spinning about an axis coincident with the axis of symmetry of the satellite to which it is affixed. The resulting equations are written for the general case so that arbitrary orientations of the spin axis with respect to the earth-satellite line and arbitrary orientations of the normal to the plate with respect to the spin axis can be treated. No attempt is made to perform the resulting integrations because of the complexity of the equations; nor is there any attempt to delineate the integration limits for the general case. However, the equations governing these limits are given. The appendixes contain: the results, in graphical form, of two representative examples; the general computer program for the calculation is given in Fortran notation; and the results of a calculation of the distribution of albedo energy on the proposed Echo II satellite. The value of the mean solar constant used is 1.395 times 10 (sup 4) ergs per centimeters-squared per second; the mean albedo of the earth is assumed to be 0.34; and the earth is assumed to be a diffuse reflector.

Modern diatom assemblages as tools for paleoenvironmental reconstruction: a case study from estuarine intertidal zones in southern Iberia

NASA Astrophysics Data System (ADS)

Gomes, Ana; Boski, Tomasz; Moura, Delminda; Szkornik, Katie; Witkowski, Andrzej; Connor, Simon; Laut, Lazaro; Sobrinho, Frederico; Oliveira, Sónia

2017-04-01

Diatoms are unicellular algae that live in saline, brackish and freshwater environments, either floating in the water column or associated with various substrates (e.g., muddy and sandy sediments). Diatoms are sensitive to changes in environmental variables such as salinity, sediment texture, nutrient availability, light and temperature. This characteristic, along with their short lifespan, allows diatoms to quickly respond to environmental changes. Since the beginning of the 20th century, diatoms have been widely used to study the Holocene evolution of estuaries worldwide, particularly to reconstruct ecological responses to sea-level and climate changes. However, diatoms have been poorly studied in estuarine intertidal zones, due to the complexity of these environments, which have both fluvial and marine influences. The aim of this study was to understand diatom diversity and spatial distribution in intertidal zones from two geomorphologically and hydrologically distinct estuaries. Sediment samples were collected from within the intertidal zones along the Arade and Guadiana River estuaries in southern Iberia. The sampling points embraced almost all the tidal and salinity gradients of both estuaries, capturing the highest possible environmental variability and hence of diatom assemblages. At each sampling point, the salinity and pH of the sediment interstitial water were measured. The sediment samples were subdivided for diatom identification, textural analysis and organic matter determination. All sampling points were georeferenced by DGPS and the duration of tidal inundation was calculated for each site. Following diatom identification, the data were analysed statistically (i.e. cluster analysis, PCA, DCA and RDA). The present study revealed that there is a great diatom diversity in both estuaries (418 species), with several species new to science. The most important diatom species (with abundances higher or equal to 5%) occur in five ecological groups, which are associated to five distinct environments: lower estuary sandflats, lower estuary mudflats, middle to upper estuary mudflats, lower estuary salt marshes and middle estuary salt marshes. This study allowed us to establish modern analogues that are essential for developing transfer functions (quantitative palaeoenvironmental estimates). These methods will enable more accurate Holocene paleoenvironmental reconstructions on the southern Iberian coast and will improve knowledge about the evolution of estuarine environments globally . The work was supported by the SFRH/BD/62405/2009 fellowship, funded by the Portuguese Foundation for Science and Technology.

Modeling the Flow of Rarefied Gases at NASA

NASA Technical Reports Server (NTRS)

Forrest E. Lumpkin, III

2012-01-01

At modest temperatures, the thermal energy of atmospheric diatomic gases such as nitrogen is primarily distributed between only translational and rotational energy modes. Furthermore, these energy modes are fully excited such that the specific heat at constant volume is well approximated by the simple expression C(sub v) = 5/2 R. As a result, classical mechanics provides a suitable approximation at such temperatures of the true quantum mechanical behavior of the inter-molecular collisions of such molecules. Using classical mechanics, the transfer of energy between rotational and translation energy modes is studied. The approach of Lordi and Mates is adopted to compute the trajectories and time dependent rotational orientations and energies during the collision of two non-polar diatomic molecules. A Monte-Carlo analysis is performed collecting data from the results of many such simulations in order to estimate the rotational relaxation time. A Graphical Processing Unit (GPU) is employed to improve the performance of the Monte-Carlo analysis. A comparison of the performance of the GPU implementation to an implementation on traditional computer architecture is made. Effects of the assumed inter-molecular potential on the relaxation time are studied. The seminar will also present highlights of computational analyses performed at NASA Johnson Space Center of heat transfer in rarefied gases.

Electron-molecule scattering in a strong laser field: Two-center interference effects

NASA Astrophysics Data System (ADS)

Dakić, J.; Habibović, D.; Čerkić, A.; Busuladžić, M.; Milošević, D. B.

2017-10-01

Laser-assisted scattering of electrons on diatomic molecules is considered using the S -matrix theory within the second Born approximation. The first term of the expansion in powers of the scattering potential corresponds to the direct or single laser-assisted scattering of electrons on molecular targets, while the second term of this expansion corresponds to the laser-assisted rescattering or double scattering. The rescattered electrons may have considerably higher energies in the final state than those that scattered only once. For multicenter polyatomic molecules scattering and rescattering may happen at any center and in any order. All these cases contribute to the scattering amplitude and the interference of different contributions leads to an increase or a decrease of the differential cross section in particular electron energy regions. For diatomic molecules there are two such contributions for single scattering and four contributions for double scattering. Analyzing the spectra of the scattered electrons, we find two interesting effects. For certain molecular orientations, the plateaus in the electron energy spectrum, characteristic of laser-assisted electron-atom scattering, are replaced by a sequence of gradually declining maxima, caused by the two-center interference effects. The second effect is the appearance of symmetric U -shaped structures in the angle-resolved energy spectra, which are described very well by the analytical formulas we provide.

Refinement of late-Early and Middle Miocene diatom biostratigraphy for the east coast of the United States

USGS Publications Warehouse

Barron, John A.; Browning, James; Sugarman, Peter; Miller, Kenneth G.

2013-01-01

Integrated Ocean Drilling Program (IODP) Expedition 313 continuously cored Lower to Middle Miocene sequences at three continental shelf sites off New Jersey, USA. The most seaward of these, Site M29, contains a well-preserved Early and Middle Miocene succession of planktonic diatoms that have been independently correlated with the geomagnetic polarity time scale derived in studies from the equatorial and North Pacific. Shallow water diatoms (species of Delphineis, Rhaphoneis, and Sceptroneis) dominate in onshore sequences in Maryland and Virginia, forming the basis for the East Coast Diatom Zones (ECDZ). Integrated study of both planktonic and shallow water diatoms in Hole M29A as well as in onshore sequences in Maryland (the Baltimore Gas and Electric Company well) and Delaware (the Ocean Drilling Program Bethany Beach corehole) allows the refinement of ECDZ zones into a high-resolution biochronology that can be successfully applied in both onshore and offshore regions of the East Coast of the United States. Strontium isotope stratigraphy supports the diatom biochronology, although for much of the Middle Miocene it suggests ages that are on average 0.4 m.y. older. The ECDZ zonal definitions are updated to include evolutionary events of Delphineis species, and regional occurrences of important planktonic diatom marker taxa are included. Updated taxonomy, reference to published figures, and photographic images are provided that will aid in the application of this diatom biostratigraphy.

Diatom assemblages promote ice formation in large lakes

PubMed Central

D'souza, N A; Kawarasaki, Y; Gantz, J D; Lee, R E; Beall, B F N; Shtarkman, Y M; Koçer, Z A; Rogers, S O; Wildschutte, H; Bullerjahn, G S; McKay, R M L

2013-01-01

We present evidence for the directed formation of ice by planktonic communities dominated by filamentous diatoms sampled from the ice-covered Laurentian Great Lakes. We hypothesize that ice formation promotes attachment of these non-motile phytoplankton to overlying ice, thereby maintaining a favorable position for the diatoms in the photic zone. However, it is unclear whether the diatoms themselves are responsible for ice nucleation. Scanning electron microscopy revealed associations of bacterial epiphytes with the dominant diatoms of the phytoplankton assemblage, and bacteria isolated from the phytoplankton showed elevated temperatures of crystallization (Tc) as high as −3 °C. Ice nucleation-active bacteria were identified as belonging to the genus Pseudomonas, but we could not demonstrate that they were sufficiently abundant to incite the observed freezing. Regardless of the source of ice nucleation activity, the resulting production of frazil ice may provide a means for the diatoms to be recruited to the overlying lake ice, thereby increasing their fitness. Bacterial epiphytes are likewise expected to benefit from their association with the diatoms as recipients of organic carbon excreted by their hosts. This novel mechanism illuminates a previously undescribed stage of the life cycle of the meroplanktonic diatoms that bloom in Lake Erie and other Great Lakes during winter and offers a model relevant to aquatic ecosystems having seasonal ice cover around the world. PMID:23552624

Intracellular metabolic pathway distribution in diatoms and tools for genome-enabled experimental diatom research.

PubMed

Gruber, Ansgar; Kroth, Peter G

2017-09-05

Diatoms are important primary producers in the oceans and can also dominate other aquatic habitats. One reason for the success of this phylogenetically relatively young group of unicellular organisms could be the impressive redundancy and diversity of metabolic isoenzymes in diatoms. This redundancy is a result of the evolutionary origin of diatom plastids by a eukaryote-eukaryote endosymbiosis, a process that implies temporary redundancy of functionally complete eukaryotic genomes. During the establishment of the plastids, this redundancy was partially reduced via gene losses, and was partially retained via gene transfer to the nucleus of the respective host cell. These gene transfers required re-assignment of intracellular targeting signals, a process that simultaneously altered the intracellular distribution of metabolic enzymes compared with the ancestral cells. Genome annotation, the correct assignment of the gene products and the prediction of putative function, strongly depends on the correct prediction of the intracellular targeting of a gene product. Here again diatoms are very peculiar, because the targeting systems for organelle import are partially different to those in land plants. In this review, we describe methods of predicting intracellular enzyme locations, highlight findings of metabolic peculiarities in diatoms and present genome-enabled approaches to study their metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Seasonal changes of diatom species in the Hooghly estuary, India

NASA Astrophysics Data System (ADS)

Goswami, P. K.

2013-12-01

The Hooghly estuary is considered as one of the most important fishing ground of north-east India which is mainly because presence of large shallow parts of Bays, which provide extensive growths for benthic and planktonic community and also makes it a highly productive area .Anthropogenic effects induce intensive pressure to this ecosystem ;and consequently results in the eutrophication followed by rapid plankton growth, sometimes even bloom. Diatom comprises one of the most diverse and significant part of the biota of aquatic habitats. Ecologically they are of immense importance since they constitute the podium of food chain and are at pinnacle of the biomass pyramid. The present study was based on the diversity of most dominant diatom species found in the brackish waters of Hooghly estuarine region in three locations of Sagar islands - Gangasagar, Chemaguri and Kachuberia. In this study diatom distribution from post monsoon - pre monsoon period was studied on the specific assemblages of them.. There was wide diversity of diatom species in different locations and in different seasons. Maximum number of diatom species was found in post-monsoon period in Gangasagar and Chemaguri, while in Kachuberia maximum number was found in pre-monsoon period. In Gangasagar, Navicula socialis, Coscinodiscus spp. and Biddulphia spp. were the predominant species in early, mid and late post monsoon period respectively and Biddulphia spp. also continues as the predominant diatom in pre-monsoon period. In Chemaguri, Amphora ostrearia, Coscinodiscus perforatus and Nitzschia acuminate were the predominant species in early, mid and late post monsoon period respectively while Coscinodiscus radiates was the stable predominant diatom species in pre-monsoon period while Thalassionema spp., Ditylum spp., Proboscia spp. and Biddulphia spp. were also found in significantly increased numbers at different times of pre-monsoon period. In Kachuberia area although a wide range of diatoms are present in post-monsoon period it was Coscinodiscus radiates which was the single predominant species found in total pre-monsoon period. Although such changes of diatom species in different seasons may be due to influence of various factors but seasonal changes may be the major factor influencing such changes of diatom species in this area.

Diatoms in sediments of perennially ice-covered Lake Hoare, and implications for interpreting lake history in the McMurdo Dry Valleys of Antarctica

USGS Publications Warehouse

Spaulding, S.A.; McKnight, Diane M.; Stoermer, E.F.; Doran, P.T.

1997-01-01

Diatom assemblages in surficial sediments, sediment cores, sediment traps, and inflowing streams of perennially ice-covered Lake Hore, South Victorialand, Antarctica were examined to determine the distribution of diatom taxa, and to ascertain if diatom species composition has changed over time. Lake Hoare is a closed-basin lake with an area of 1.8 km2, maximum depth of 34 m, and mean depth of 14 m, although lake level has been rising at a rate of 0.09 m yr-1 in recent decades. The lake has an unusual regime of sediment deposition: coarse grained sediments accumulate on the ice surface and are deposited episodically on the lake bottom. Benthic microbial mats are covered in situ by the coarse episodic deposits, and the new surfaces are recolonized. Ice cover prevents wind-induced mixing, creating the unique depositional environment in which sediment cores record the history of a particular site, rather than a lake=wide integration. Shallow-water (<1 m) diatom assemblages (Stauroneis anceps, Navicula molesta, Diadesmis contenta var. parallela, Navicula peraustralis) were distinct from mid-depth (4-16 m) assemblages (Diadesmis contenta, Luticola muticopsis fo. reducta, Stauroneis anceps, Diadesmis contenta var. parallela, Luticola murrayi) and deep-water (2-31 m) assemblages (Luticola murrayi, Luticola muticopsis fo. reducta, Navicula molesta. Analysis of a sediment core (30 cm long, from 11 m water depth) from Lake Hoare revealed two abrupt changes in diatom assemblages. The upper section of the sediment core contained the greatest biomass of benthic microbial mat, as well as the greatest total abundance and diversity of diatoms. Relative abundances of diatoms in this section are similar to the surficial samples from mid-depths. An intermediate zone contained less organic material and lower densities of diatoms. The bottom section of core contained the least amount of microbial mat and organic material, and the lowest density of diatoms. The dominant process influencing species composition and abundance of diatom assemblages in the benthic microbial mats is episodic deposition of coarse sediment from the ice surface.

Analysis of Elastic and Electrical Fields in Quantum Structures by Novel Green’s Functions and Related Boundary Integral Methods

DTIC Science & Technology

2010-12-01

arbitrarily shaped polygon QWR inclusion/inhomogeneity with eigenstrain ∗Ijγ in an anisotropic substrate... eigenstrain *ijγ is applied to the QWR which is an arbitrarily shaped polygon .................................. 42 3.2 A square InAs QWR embedded in...the QWR domain V and to 0 outside. Figure 2.1 An arbitrarily shaped polygon QWR inclusion/inhomogeneity with eigenstrain ∗Ijγ in an anisotropic

The transferability of diatoms to clothing and the methods appropriate for their collection and analysis in forensic geoscience.

PubMed

Scott, Kirstie R; Morgan, Ruth M; Jones, Vivienne J; Cameron, Nigel G

2014-08-01

Forensic geoscience is concerned with the analysis of geological materials in order to compare and exclude environmental samples from a common source, or to identify an unknown provenance in a criminal investigation. Diatom analysis is currently an underused technique within the forensic geoscience approach, which has the potential to provide an independent ecological assessment of trace evidence. This study presents empirical data to provide a preliminary evidence base in order to be able to understand the nature of diatom transfers to items of clothing, and the collection of transferred diatom trace evidence from a range of environments under experimental conditions. Three diatom extraction methods were tested on clothing that had been in contact with soil and water sites: rinsing in water (RW), rinsing in ethanol (RE), and submersion in H2O2 solution (H). Scanning electron microscopy (S.E.M.) analysis was undertaken in order to examine the degree of diatom retention on treated clothing samples. The total diatom yield and species richness data was recorded from each experimental sample in order to compare the efficacy of each method in collecting a representative sample for analysis. Similarity was explored using correspondence analysis. The results highlight the efficiency of H2O2 submersion in consistently extracting high diatom counts with representative species from clothing exposed to both aquatic and terrestrial sites. This is corroborated by S.E.M. analysis. This paper provides an important empirical evidence base for both establishing that diatoms do indeed transfer to clothing under forensic conditions in a range of environments, and in identifying that H2O2 extraction is the most efficient technique for the optimal collection of comparative samples. There is therefore potentially great value in collecting and analysing diatom components of geoforensic samples in order to aid in forensic investigation. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

The effects of hydrological dynamics on benthic diatom community structure in a highly stratified estuary: The case of the Ebro Estuary (Catalonia, Spain)

NASA Astrophysics Data System (ADS)

Rovira, L.; Trobajo, R.; Leira, M.; Ibáñez, C.

2012-04-01

This study of the distribution of benthic diatom assemblages and their relationship with environmental factors in a highly stratified Mediterranean estuary, i.e. the Ebro Estuary, shows the importance of hydrological dynamics to explain the features of the diatom community in such an estuary, where river flow magnitude and fluctuations imply strong physicochemical variability especially in sites close to the sea. Eight sites along the estuary were sampled during 2007-2008 both at superficial and deep water layers, in order to gather both horizontal and vertical estuarine physicochemical and hydrological gradients. Canonical Variates Analysis and Hierarchical Cluster Analysis segregated diatom community in two assemblages depending on the dynamics of the salt-wedge. The diatom assemblages of riverine conditions (i.e. without salt-wedge influence) where characterised by high abundances of Cocconeis placentula var. euglypta and Amphora pediculus, meanwhile high abundances of Nizschia frustulum and Nitzschia inconspicua were characteristic of estuarine conditions (i.e. under salt-wedge influence). Redundancy Analysis showed that both diatom assemblages responded seasonally to Ebro River flows, especially in estuarine conditions, where fluctuating conditions affected diatom assemblages both at spatial and temporal scale.

Current trends to comprehend lipid metabolism in diatoms.

PubMed

Zulu, Nodumo Nokulunga; Zienkiewicz, Krzysztof; Vollheyde, Katharina; Feussner, Ivo

2018-04-01

Diatoms are the most dominant phytoplankton species in oceans and they continue to receive a great deal of attention because of their significant contributions in ecosystems and the environment. Due to triacylglycerol (TAG) profiles that are abundant in medium-chain fatty acids, diatoms have emerged to be better feed stocks for biofuel production, in comparison to the commonly studied green microalgal species (chlorophytes). Importantly, diatoms are also known for their high levels of the essential ω3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and are considered to be a promising alternative source of these components. The two most commonly exploited diatoms include Thalassiosira pseudonana and Phaeodactylum tricornutum. Although obvious similarities between diatoms and chlorophytes exist, there are some substantial differences in their lipid metabolism. This review provides an overview on lipid metabolism in diatoms, with P. tricornutum as the most explored model. Special emphasis is placed on the synthesis and incorporation of very long chain ω3 fatty acids into lipids. Furthermore, current approaches including genetic engineering and biotechnological methods aimed at improving and maximizing lipid production in P. tricornutum are also discussed. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

[Distribution of diatoms in central city of Beijing].

PubMed

Li, Li-Ping; Sun, Ting-Yi; Liu, Hong-Xia; Zhang, Hai-Dong; Bai, Ying-Jie; Wang, Rong-Shuai; Liu, Liang

2012-08-01

To explore the quantity and distribution of diatoms in main rivers and lakes in Xicheng, Dongcheng, Chaoyang, Haidian, Fengtai and Shijingshan Districts of the city of Beijing. Water samples were examined through the method of disorganizing, which were collected from 16 rivers and lakes in the central city of Beijing in September and October 2011. Diatom species and proportions of water samples were analyzed using DotSlide microscope station. A total of 10 species of diatoms were detected. Cyclotella, Synedra and Melosira etc. were found to be the dominant species via quantitative analysis. Significant differences were observed for diatom species and proportions among the different rivers and lakes. Melosira was found to be the dominant species in the Chang River; Synedra, in the Zhuan River, the Kunyu River and the Taoranting Park; Cyclotella, in the East Moat River, the Ba River, the Liangshui River and the Yongding River; and Navicula, in the Liangma River; Nitzschia, in the diversion canal of the Yongding River. The features of distribution of diatoms in the central city of Beijing are outlined. The morphological and relative constituent ratio database of diatoms are established in central city of Beijing.

Succession of Pelagic Organisms in the Size Range 0·5-200 μm During a Diatom Bloom in Otsuchi Bay, Japan

NASA Astrophysics Data System (ADS)

Tsuda, Atsushi; Sugisaki, Hiroya; Takahashi, Koji; Furuya, Ken

1994-08-01

The succession of pelagic organisms in the approximate size range 0·5-200 μm was investigated during a spring diatom bloom in Otsuchi Bay on the Pacific coast of northern Japan. The diatom bloom lasted 3 weeks in the middle of the period examined. The study period was divided into three phases: pre-bloom, bloom and post-bloom. Mesodinium rubrum, an autotrophic ciliate, was abundant in the pre-bloom phase, when vertical mixing was intense. During the bloom phase, the biomass of organisms other than diatoms themselves and bacteria was depressed. A bacterial peak was observed 4 days after the diatom peak and peaks of nano-autotrophs and -heterotrophs occurred after 14 days. Phototrophic picoplankton showed a biomass peak at the same time as nanoplankton. Grazing on diatoms by the copepod population was shown by the occurrences of faecal pellets and copepod nauplii during and after the bloom phase. These results suggest that production of copepods and bacteria depended only on the diatom bloom directly, and that heterotrophic micro-protista depended on the production of pico- and nano-autotrophs in the post-bloom phase.

Loosely-Bound Diatomic Molecules.

ERIC Educational Resources Information Center

Balfour, W. J.

1979-01-01

Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

Robustness of the filamentation instability in arbitrarily oriented magnetic field: Full three dimensional calculation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bret, A., E-mail: antoineclaude.bret@uclm.es

2014-02-15

The filamentation (Weibel) instability plays a key role in the formation of collisionless shocks which are thought to produce Gamma-Ray-Bursts and High-Energy-Cosmic-Rays in astrophysical environments. While it has been known for long that a flow-aligned magnetic field can completely quench the instability, it was recently proved in 2D that in the cold regime, such cancelation is possible if and only if the field is perfectly aligned. Here, this result is finally extended to a 3D geometry. Calculations are conducted for symmetric and asymmetric counter-streaming relativistic plasma shells. 2D results are retrieved in 3D: the instability can never be completely canceledmore » for an oblique magnetic field. In addition, the maximum growth-rate is always larger for wave vectors lying in the plan defined by the flow and the oblique field. On the one hand, this bears consequences on the orientation of the generated filaments. On the other hand, it certifies 2D simulations of the problem can be performed without missing the most unstable filamentation modes.« less

Radiation from a current filament driven by a traveling wave

NASA Technical Reports Server (NTRS)

Levine, D. M.; Meneghini, R.

1976-01-01

Solutions are presented for the electromagnetic fields radiated by an arbitrarily oriented current filament located above a perfectly conducting ground plane and excited by a traveling current wave. Both an approximate solution, valid in the fraunhofer region of the filament and predicting the radiation terms in the fields, and an exact solution, which predicts both near and far field components of the electromagnetic fields, are presented. Both solutions apply to current waveforms which propagate along the channel but are valid regardless of the actual waveshape. The exact solution is valid only for waves which propagate at the speed of light, and the approximate solution is formulated for arbitrary velocity of propagation. The spectrum-magnitude of the fourier transform-of the radiated fields is computed by assuming a compound exponential model for the current waveform. The effects of channel orientation and length, as well as velocity of propagation of the current waveform and location of the observer, are discussed. It is shown that both velocity of propagation and an effective channel length are important in determining the shape of the spectrum.

Diamond-Based Magnetic Imaging with Fourier Optical Processing

NASA Astrophysics Data System (ADS)

Backlund, Mikael P.; Kehayias, Pauli; Walsworth, Ronald L.

2017-11-01

Diamond-based magnetic field sensors have attracted great interest in recent years. In particular, wide-field magnetic imaging using nitrogen-vacancy (NV) centers in diamond has been previously demonstrated in condensed matter, biological, and paleomagnetic applications. Vector magnetic imaging with NV ensembles typically requires a significant applied field (>10 G ) to resolve the contributions from four crystallographic orientations, hindering studies of magnetic samples that require measurement in low or independently specified bias fields. Here we model and measure the complex amplitude distribution of NV emission at the microscope's Fourier plane and show that by modulating this collected light at the Fourier plane, one can decompose the NV ensemble magnetic resonance spectrum into its constituent orientations by purely optical means. This decomposition effectively extends the dynamic range at a given bias field and enables wide-field vector magnetic imaging at arbitrarily low bias fields, thus broadening potential applications of NV imaging and sensing. Our results demonstrate that NV-based microscopy stands to benefit greatly from Fourier optical approaches, which have already found widespread utility in other branches of microscopy.

A program to calculate pulse transmission responses through transversely isotropic media

NASA Astrophysics Data System (ADS)

Li, Wei; Schmitt, Douglas R.; Zou, Changchun; Chen, Xiwei

2018-05-01

We provide a program (AOTI2D) to model responses of ultrasonic pulse transmission measurements through arbitrarily oriented transversely isotropic rocks. The program is built with the distributed point source method that treats the transducers as a series of point sources. The response of each point source is calculated according to the ray-tracing theory of elastic plane waves. The program could offer basic wave parameters including phase and group velocities, polarization, anisotropic reflection coefficients and directivity patterns, and model the wave fields, static wave beam, and the observed signals for pulse transmission measurements considering the material's elastic stiffnesses and orientations, sample dimensions, and the size and positions of the transmitters and the receivers. The program could be applied to exhibit the ultrasonic beam behaviors in anisotropic media, such as the skew and diffraction of ultrasonic beams, and analyze its effect on pulse transmission measurements. The program would be a useful tool to help design the experimental configuration and interpret the results of ultrasonic pulse transmission measurements through either isotropic or transversely isotropic rock samples.

Near Zone: Basic scattering code user's manual with space station applications

NASA Technical Reports Server (NTRS)

Marhefka, R. J.; Silvestro, J. W.

1989-01-01

The Electromagnetic Code - Basic Scattering Code, Version 3, is a user oriented computer code to analyze near and far zone patterns of antennas in the presence of scattering structures, to provide coupling between antennas in a complex environment, and to determine radiation hazard calculations at UHF and above. The analysis is based on uniform asymptotic techniques formulated in terms of the Uniform Geometrical Theory of Diffraction (UTD). Complicated structures can be simulated by arbitrarily oriented flat plates and an infinite ground plane that can be perfectly conducting or dielectric. Also, perfectly conducting finite elliptic cylinder, elliptic cone frustum sections, and finite composite ellipsoids can be used to model the superstructure of a ship, the body of a truck, and airplane, a satellite, etc. This manual gives special consideration to space station modeling applications. This is a user manual designed to give an overall view of the operation of the computer code, to instruct a user in how to model structures, and to show the validity of the code by comparing various computed results against measured and alternative calculations such as method of moments whenever available.

Bacteria Interactions with Dying Diatoms

NASA Astrophysics Data System (ADS)

Smriga, S.; Juarez, G.; Fernandez, V.; Stocker, R.

2016-02-01

Dying phytoplankton are surrounded by microscale gradients of dissolved organic matter (DOM) that can attract bacteria. These 'phycospheres' may impact the trophic transfer of DOM in the marine microbial food web and enable the growth of bacterial populations, yet these effects remain poorly quantified particularly in relation to the physiological state of the phytoplankton. We dissected phycosphere interactions at unprecedented spatial and temporal resolution using the model diatom Thalassiosira weissflogii and the bacterium Marinobacter adhaerans. Diatom stress was stimulated by addition of polyunsaturated aldehyde (PUA) and both diatom and bacterial responses were captured via time-lapse fluorescence microscopy. We found that stressed diatoms underwent lysis 10-15 h after PUA treatment. Coordinated with the timing of this transition into phytodetritus, wild-type Marinobacter accumulated via chemotaxis near the diatoms immediately following lysis. In contrast, at lysis there was no accumulation of either a non-chemotactic or a non-motile mutant of Marinobacter, pointing to behavioral rather than demographic responses as drivers for the accumulation. Despite the lack of response, non-chemotactic as well as non-swimming bacterial cells that by chance attached to or were located near (<30 µm) stressed diatoms experienced more growth than cells further afield. Growth within the phycosphere was even greater after diatom lysis. Through quantification at the microscale, these results reveal that chemotaxis may precede rapid bacterial attachment to stressed and dying diatoms and may be integral to the microbial colonization of new phytodetritus during phytoplankton blooms and bloom collapses in coastal ecosystems. Even while chemotactic cells retain a growth advantage given their ability to sense and respond to lysis events, phycosphere DOM provides growth benefits to both motile and non-motile taxa that become attached to or happen to be co-located with new phytodetrital particles, thus likely influencing the composition of particle-attached microbial communities.

Development of the initial diatom microfouling layer on antifouling and fouling-release surfaces in temperate and tropical Australia.

PubMed

Molino, Paul J; Campbell, Ewan; Wetherbee, Richard

2009-11-01

Diatoms are a major component of the slime layers that form on artificial surfaces in marine environments. In this article, the role played by diatoms during the pioneering stages of colonization of three marine antifouling (AF) coatings, viz Intersmooth 360, Super Yacht 800 and a fouling-release (FR) coating Intersleek 700, was investigated. The study was conducted over three distinct seasons in two very different marine environments in Australia, ie temperate Williamstown, Victoria and tropical Cairns, Queensland. Diatom fouling occurred more rapidly on the FR coating Intersleek 700, compared to both biocidal AF paints. However, colonization by diatoms on all three coatings was generally slow during the 16-day study. Benthic diatoms do not subsist by floating around in the water column, rather they only gain the opportunity to colonize new surfaces when they either voluntarily release or are displaced from their benthic habitat, thereafter entering the water column where the opportunity to adhere to a new surface presents itself. However, once settled, fouling diatoms grow exponentially from the site of attachment, spreading out until they populate large areas of the surface. This mode of surface colonization correlates more with an 'infection' type, epidemiology model, a mechanism that accounts for the colonization of significant regions of the coating surface from a single fouling diatom cell, forming 'clonal patches'. This is in comparison to the bacterial colonization of the surface, which exhibits far more rapid recruitment and growth of cells on the substratum surface. Therefore, it is hypothesized that fouling diatoms may be characterized more by their ability to adhere and grow on surfaces already modified by bacterial biofilms, rather than on their strength of adhesion. Cell morphology and the ability to avoid shear may also be an important factor.

Continuous Silicate Utilization Over Multiple 14L:10D Day:Night Cycles Confirms Night Metabolism in Lake Michigan Diatom Enrichments Using Either Nitrate or Ammonium as a Nitrogen Source

NASA Astrophysics Data System (ADS)

Soderling, M.; Aguilar, C.; Cuhel, R. L.

2016-02-01

Diatoms are single-celled organelle containing eukaryotes living in "glass houses". As diatoms only take up silica when they replicate, measuring the amounts of dissolved and particulate silicate were an important aspect of this study. Silica was used as a proxy of the diatom reproduction. Depending on growth conditions, some algal species divide throughout the day and night; this suggests that protein synthesis can be an important component of algal night metabolism and hence nitrogen utilization. The goal of this experiment was to measure the amount of night protein synthesis occurring in a culture of diatoms from Lake Michigan. Diatoms were enriched with light for energy and excess nutrients—including phosphate, silicate, nitrate and limited ammonium for some—along with use of physical separation methods. Growing conditions were prepared in a way which anticipated the diatoms would synchronize to a 14:10 day/night cycle and store energy, during their day phase, to use for night protein synthesis and replication. Their growth was monitored by taking samples before and after the transitions of light to dark along with midday and midnight samples. Assays of dissolved and particulate silicate were used to measure utilization, which confirmed their nighttime growth. As hypothesized, the diatoms had significant growth during their night phase. There were decreases in the nighttime dissolved silicate and increases in the nighttime particulate silicate. When available, the diatoms preferred to use ammonium instead of nitrate. Cell division during the night phase indicated sufficient daytime energy storage to fuel night protein synthesis and cell replication. Uptake of nutrients occurred at night almost as if the "sun" did not set. There was continuous growth of this photosynthetic community.

Development of a diatom-based multimetric index for acid mine drainage impacted depressional wetlands.

PubMed

Riato, Luisa; Leira, Manel; Della Bella, Valentina; Oberholster, Paul J

2018-01-15

Acid mine drainage (AMD) from coal mining in the Mpumalanga Highveld region of South Africa has caused severe chemical and biological degradation of aquatic habitats, specifically depressional wetlands, as mines use these wetlands for storage of AMD. Diatom-based multimetric indices (MMIs) to assess wetland condition have mostly been developed to assess agricultural and urban land use impacts. No diatom MMI of wetland condition has been developed to assess AMD impacts related to mining activities. Previous approaches to diatom-based MMI development in wetlands have not accounted for natural variability. Natural variability among depressional wetlands may influence the accuracy of MMIs. Epiphytic diatom MMIs sensitive to AMD were developed for a range of depressional wetland types to account for natural variation in biological metrics. For this, we classified wetland types based on diatom typologies. A range of 4-15 final metrics were selected from a pool of ~140 candidate metrics to develop the MMIs based on their: (1) broad range, (2) high separation power and (3) low correlation among metrics. Final metrics were selected from three categories: similarity to reference sites, functional groups, and taxonomic composition, which represent different aspects of diatom assemblage structure and function. MMI performances were evaluated according to their precision in distinguishing reference sites, responsiveness to discriminate reference and disturbed sites, sensitivity to human disturbances and relevancy to AMD-related stressors. Each MMI showed excellent discriminatory power, whether or not it accounted for natural variation. However, accounting for variation by grouping sites based on diatom typologies improved overall performance of MMIs. Our study highlights the usefulness of diatom-based metrics and provides a model for the biological assessment of depressional wetland condition in South Africa and elsewhere. Copyright © 2017 Elsevier B.V. All rights reserved.

[Comparative analysis between diatom nitric acid digestion method and plankton 16S rDNA PCR method].

PubMed

Han, Jun-ge; Wang, Cheng-bao; Li, Xing-biao; Fan, Yan-yan; Feng, Xiang-ping

2013-10-01

To compare and explore the application value of diatom nitric acid digestion method and plankton 16S rDNA PCR method for drowning identification. Forty drowning cases from 2010 to 2011 were collected from Department of Forensic Medicine of Wenzhou Medical University. Samples including lung, kidney, liver and field water from each case were tested with diatom nitric acid digestion method and plankton 16S rDNA PCR method, respectively. The Diatom nitric acid digestion method and plankton 16S rDNA PCR method required 20 g and 2 g of each organ, and 15 mL and 1.5 mL of field water, respectively. The inspection time and detection rate were compared between the two methods. Diatom nitric acid digestion method mainly detected two species of diatoms, Centriae and Pennatae, while plankton 16S rDNA PCR method amplified a length of 162 bp band. The average inspection time of each case of the Diatom nitric acid digestion method was (95.30 +/- 2.78) min less than (325.33 +/- 14.18) min of plankton 16S rDNA PCR method (P < 0.05). The detection rates of two methods for field water and lung were both 100%. For liver and kidney, the detection rate of plankton 16S rDNA PCR method was both 80%, higher than 40% and 30% of diatom nitric acid digestion method (P < 0.05), respectively. The laboratory testing method needs to be appropriately selected according to the specific circumstances in the forensic appraisal of drowning. Compared with diatom nitric acid digestion method, plankton 16S rDNA PCR method has practice values with such advantages as less quantity of samples, huge information and high specificity.

Response of Spring Diatoms to CO2 Availability in the Western North Pacific as Determined by Next-Generation Sequencing.

PubMed

Endo, Hisashi; Sugie, Koji; Yoshimura, Takeshi; Suzuki, Koji

2016-01-01

Next-generation sequencing (NGS) technologies have enabled us to determine phytoplankton community compositions at high resolution. However, few studies have adopted this approach to assess the responses of natural phytoplankton communities to environmental change. Here, we report the impact of different CO2 levels on spring diatoms in the Oyashio region of the western North Pacific as estimated by NGS of the diatom-specific rbcL gene (DNA), which encodes the large subunit of RubisCO. We also examined the abundance and composition of rbcL transcripts (cDNA) in diatoms to assess their physiological responses to changing CO2 levels. A short-term (3-day) incubation experiment was carried out on-deck using surface Oyashio waters under different pCO2 levels (180, 350, 750, and 1000 μatm) in May 2011. During the incubation, the transcript abundance of the diatom-specific rbcL gene decreased with an increase in seawater pCO2 levels. These results suggest that CO2 fixation capacity of diatoms decreased rapidly under elevated CO2 levels. In the high CO2 treatments (750 and 1000 μatm), diversity of diatom-specific rbcL gene and its transcripts decreased relative to the control treatment (350 μatm), as well as contributions of Chaetocerataceae, Thalassiosiraceae, and Fragilariaceae to the total population, but the contributions of Bacillariaceae increased. In the low CO2 treatment, contributions of Bacillariaceae also increased together with other eukaryotes. These suggest that changes in CO2 levels can alter the community composition of spring diatoms in the Oyashio region. Overall, the NGS technology provided us a deeper understanding of the response of diatoms to changes in CO2 levels in terms of their community composition, diversity, and photosynthetic physiology.

Molecular insights into the novel aspects of diatom biology.

PubMed

Scala, S; Bowler, C

2001-10-01

Diatoms are unicellular photosynthetic eukaryotes that are thought to contribute as much as 25% of global primary productivity. In spite of their ecological importance in the worlds oceans, very little information is available at the molecular level about the novel aspects of their biology. Recent advances, such as the development of gene transfer protocols, are now allowing the genetic dissection of diatom biology. Notable examples are advances in understanding the genetic basis for the silica-based bioinorganic pattern formation of their cell walls and for elucidating key aspects of diatom ecophysiology. The potentiation of current research will allow an evaluation of the use of diatoms to construct submicrometre-scale silicon structures for the nanotechnology industry and will reveal the molecular secrets underlying their ecological success.

Diatoms in comets

NASA Technical Reports Server (NTRS)

Hoover, R.; Hoyle, F.; Wallis, M. K.; Wickramasinghe, N. C.

1986-01-01

The fossil record of the microscopic algae classified as diatoms suggests they were injected to earth at the Cretaceous boundary. Not only could diatoms remain viable in the cometary environment, but also many species might replicate in illuminated surface layers or early interior layers of cometary ice. Presumably they reached the solar system on an interstellar comet as an already-evolved assemblage of organisms. Diatoms might cause color changes to comet nuclei while their outgassing decays and revives around highly elliptical orbits. Just as for interstellar absorption, high-resolution IR observations are capable of distinguishing whether the 10-micron feature arises from siliceous diatom material or mineral silicates. The 10-30-micron band and the UV 220-nm region can also provide evidence of biological material.

Watershed Alteration Impacts to Benthic Diatom Assemblages in Streams

EPA Science Inventory

To examine the use of diatoms as indicators of urban impacts to streams, we identified relationships of diatom assemblages with water chemistry and land use for 160 sites in New England. The first axis of a nonmetric multidimensional scaling ordination showed significant relation...

Development of diatom indicators of ecological conditons for streams of the western US

EPA Science Inventory

The species composition of benthic diatoms was related to environmental conditions in streams throughout the western US to develop diatom traits, indicators for assessment of biological condition and indicators for diagnosing stressors. We hypothesized that indicators based on s...

Development of diatom indicators of ecological conditions for streams of the western US

EPA Science Inventory

The species composition of benthic diatoms was related to environmental conditions in streams throughout the western US to develop diatom traits, indicators for assessment of biological condition and indicators for diagnosing stressors. We hypothesized that indicators based on sp...

Diatomic Spectral Database

National Institute of Standards and Technology Data Gateway

SRD 114 Diatomic Spectral Database (Web, free access)   All of the rotational spectral lines observed and reported in the open literature for 121 diatomic molecules have been tabulated. The isotopic molecular species, assigned quantum numbers, observed frequency, estimated measurement uncertainty, and reference are given for each transition reported.

Are biotic indices sensitive to river toxicants? A comparison of metrics based on diatoms and macro-invertebrates.

PubMed

Blanco, S; Bécares, E

2010-03-01

Biotic indices based on macro-invertebrates and diatoms are frequently used to diagnose ecological quality in watercourses, but few published works have assessed their effectiveness as biomonitors of the concentration of micropollutants. A biological survey performed at 188 sites in the basin of the River Duero in north-western Spain. Nineteen diatom and six macro-invertebrate indices were calculated and compared with the concentrations of 37 different toxicants by means of a correlation analysis. Several chemical variables analysed correlated significantly with at least one biotic index. Sládecek's diatom index and the number of macro-invertebrate families exhibited particularly high correlation coefficients. Methods based on macro-invertebrates performed better in detecting biocides, while diatom indices showed stronger correlations with potentially toxic elements such as heavy metals. All biotic indices, and particularly diatom indices, were especially sensitive to the concentration of fats and oils and trichloroethene. Copyright 2010 Elsevier Ltd. All rights reserved.

Diatom diversity and response in metal-polluted river environment: preliminary reports from Gromolo Torrent (Liguria, Italy)

NASA Astrophysics Data System (ADS)

Capello, Marco; Tolotti, Raffaella; Bernabè, Dimitri; Carbone, Cristina; Consani, Sirio; Vagge, Greta; Cutroneo, Laura

2016-04-01

Mineral content and physico-chemical properties of the freshwaters are the main factors affecting both algal assemblages and distributions, while presence of dissolved silicon, low water conductivity, and rocky-mountain habitats host benthic diatom assemblages of high species richness. It is shown that diatoms are sensible to the freshwater acidification (used as pH indicators in acid waters), environmental and climate changes, river organic load, and heavy metal water pollution. For this characteristic, diatoms are among the major biological markers for a variety of environmental and stratigraphic applications. In particular, qualitative and quantitative analyses (assemblage analyses) together with biotic indices as well as morphological and ultrastructure parameterisation provide tools for detailed environmental control and paleo-environmental reconstructions. Severe environmental problems are typically caused by "abandoned mine" and are consequences of the cessation of the mining activity with a lack in infrastructure maintenance. The mine waters which flow into the Gromolo Torrent are almost acidic (pH varying from 2.4 to 5) and enriched in heavy metals and SO42-. This pollution is caused by Acid Mine Drainage (AMD) processes that interest the Libiola mining area, known as a typical example of active AMD processes. The aim of this work is: 1) to characterise the local benthic diatom assemblages along the acidic mine effluents that discharge from Libiola mine, the entire Gromolo torrent course, and in the marine area off the torrent mouth; 2) to identify the main diatom biomarker taxa; 3) to highlight striking situations of equilibrium-disequilibrium in the algal communities, and 4) to point out types and frequency of some teratologies affecting specific diatom taxa as a response to environmental stressors (such as metal-metalloid enrichment). A total of 17 diatom samples was collected and examined, including some marine samples. Diatoms were collected in the riverbed from the hard surface of selected cobblestone by scraping. In laboratory all the samples were washed (by digestion with hydrogen peroxide) and mounted according to the protocol used by the DISTAV Laboratories (University of Genoa). Identification and enumeration of diatom valves was performed using an LM Reichert Jung-Polyvar microscope with 1000x oil-immersion lens. Moreover, a representative subsample of each preparation was observed using SEM images providing an interesting iconographic dataset. Preliminary results show that diatom assemblages are characteristic (in both quality and quantity) in the three different environmental conditions highlighted: a) in AMD environment diatoms are quantitatively scarcely, represented by both typically pioneer and highly tolerant species; b) in the Gromolo torrent diatoms are well represented with fairly well-structured communities, but present specific types and different frequencies in teratological frustula, whereas c) in marine environment they are very poorly represented.

Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii

PubMed Central

Gärdes, Astrid; Iversen, Morten H; Grossart, Hans-Peter; Passow, Uta; Ullrich, Matthias S

2011-01-01

Aggregation of algae, mainly diatoms, is an important process in marine systems leading to the settling of particulate organic carbon predominantly in the form of marine snow. Exudation products of phytoplankton form transparent exopolymer particles (TEP), which acts as the glue for particle aggregation. Heterotrophic bacteria interacting with phytoplankton may influence TEP formation and phytoplankton aggregation. This bacterial impact has not been explored in detail. We hypothesized that bacteria attaching to Thalassiosira weissflogii might interact in a yet-to-be determined manner, which could impact TEP formation and aggregate abundance. The role of individual T. weissflogii-attaching and free-living new bacterial isolates for TEP production and diatom aggregation was investigated in vitro. T. weissflogii did not aggregate in axenic culture, and striking differences in aggregation dynamics and TEP abundance were observed when diatom cultures were inoculated with either diatom-attaching or free-living bacteria. The data indicated that free-living bacteria might not influence aggregation whereas bacteria attaching to diatom cells may increase aggregate formation. Interestingly, photosynthetically inactivated T. weissflogii cells did not aggregate regardless of the presence of bacteria. Comparison of aggregate formation, TEP production, aggregate sinking velocity and solid hydrated density revealed remarkable differences. Both, photosynthetically active T. weissflogii and specific diatom-attaching bacteria were required for aggregation. It was concluded that interactions between heterotrophic bacteria and diatoms increased aggregate formation and particle sinking and thus may enhance the efficiency of the biological pump. PMID:20827289

Metatranscriptome analyses indicate resource partitioning between diatoms in the field.

PubMed

Alexander, Harriet; Jenkins, Bethany D; Rynearson, Tatiana A; Dyhrman, Sonya T

2015-04-28

Diverse communities of marine phytoplankton carry out half of global primary production. The vast diversity of the phytoplankton has long perplexed ecologists because these organisms coexist in an isotropic environment while competing for the same basic resources (e.g., inorganic nutrients). Differential niche partitioning of resources is one hypothesis to explain this "paradox of the plankton," but it is difficult to quantify and track variation in phytoplankton metabolism in situ. Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that cooccur regularly in an estuary on the east coast of the United States (Narragansett Bay). Expression of known N and P metabolic pathways varied between diatoms, indicating apparent differences in resource utilization capacity that may prevent direct competition. Nutrient amendment incubations skewed N/P ratios, elucidating nutrient-responsive patterns of expression and facilitating a quantitative comparison between diatoms. The resource-responsive (RR) gene sets deviated in composition from the metabolic profile of the organism, being enriched in genes associated with N and P metabolism. Expression of the RR gene set varied over time and differed significantly between diatoms, resulting in opposite transcriptional responses to the same environment. Apparent differences in metabolic capacity and the expression of that capacity in the environment suggest that diatom-specific resource partitioning was occurring in Narragansett Bay. This high-resolution approach highlights the molecular underpinnings of diatom resource utilization and how cooccurring diatoms adjust their cellular physiology to partition their niche space.

Further Evaluation of Diatom Periphyton as Indicators of Cultivation and Grazing Impairment in Montana Wetlands

EPA Pesticide Factsheets

As a follow up report to a 1999 study, this report is an analysis of diatom assemblages from 24 sites at two locations in order to evaluate the potential of diatoms as indicators of impairment due to cultivation and grazing.

Diatom Communities and Metrics as Indicators of Urbanization Effects on Streams and Potential Moderation by Landscape Green Infrastructure

EPA Science Inventory

Diatoms are very useful and important indicators of anthropogenic impacts on streams because they are the foundation of primary production and are responsive to nutrients, conductivity, and habitat conditions. We characterized relationships of diatom assemblages with water chemis...

DIATOM INDICES OF STREAM ECOSYSTEM CONDITIONS: COMPARISON OF GENUS VS. SPECIES LEVEL IDENTIFICATIONS

EPA Science Inventory

Diatom assemblage data collected between 1993 and 1995 from 233 Mid-Appalachian streams were used to compare indices of biotic integrity based on genus vs. species level taxonomy. Thirty-seven genera and 197 species of diatoms were identified from these samples. Metrics included...

Silica diatom shells tailored with Au nanoparticles enable sensitive analysis of molecules for biological, safety and environment applications.

PubMed

Onesto, V; Villani, M; Coluccio, M L; Majewska, R; Alabastri, A; Battista, E; Schirato, A; Calestani, D; Coppedé, N; Cesarelli, M; Amato, F; Di Fabrizio, E; Gentile, F

2018-04-10

Diatom shells are a natural, theoretically unlimited material composed of silicon dioxide, with regular patterns of pores penetrating through their surface. For their characteristics, diatom shells show promise to be used as low cost, highly efficient drug carriers, sensor devices or other micro-devices. Here, we demonstrate diatom shells functionalized with gold nanoparticles for the harvesting and detection of biological analytes (bovine serum albumin-BSA) and chemical pollutants (mineral oil) in low abundance ranges, for applications in bioengineering, medicine, safety, and pollution monitoring.

The effects of fine-scale substratum roughness on diatom community structure in estuarine biofilms.

PubMed

Sweat, L Holly; Johnson, Kevin B

2013-09-01

Benthic diatoms are a major component of biofilms that form on surfaces submerged in marine environments. Roughness of the underlying substratum affects the settlement of both diatoms and subsequent macrofouling colonizers. This study reports the effects of roughness on estuarine diatom communities established in situ in the Indian River Lagoon, FL, USA. Natural communities were established on acrylic panels with a range of surface roughnesses. Smoother substrata exhibited higher cell density, species richness, and diversity. Twenty-three of 58 species were found either exclusively or more abundantly on the smooth surfaces compared to one or both roughened treatments. The results suggest a greater ability of benthic diatoms to recruit and colonize smooth surfaces, which is probably explained by a higher degree of contact between the cells and the surface.

Interactions between Benthic Copepods, Bacteria and Diatoms Promote Nitrogen Retention in Intertidal Marine Sediments

PubMed Central

Stock, Willem; Heylen, Kim; Sabbe, Koen; Willems, Anne; De Troch, Marleen

2014-01-01

The present study aims at evaluating the impact of diatoms and copepods on microbial processes mediating nitrate removal in fine-grained intertidal sediments. More specifically, we studied the interactions between copepods, diatoms and bacteria in relation to their effects on nitrate reduction and denitrification. Microcosms containing defaunated marine sediments were subjected to different treatments: an excess of nitrate, copepods, diatoms (Navicula sp.), a combination of copepods and diatoms, and spent medium from copepods. The microcosms were incubated for seven and a half days, after which nutrient concentrations and denitrification potential were measured. Ammonium concentrations were highest in the treatments with copepods or their spent medium, whilst denitrification potential was lowest in these treatments, suggesting that copepods enhance dissimilatory nitrate reduction to ammonium over denitrification. We hypothesize that this is an indirect effect, by providing extra carbon for the bacterial community through the copepods' excretion products, thus changing the C/N ratio in favour of dissimilatory nitrate reduction. Diatoms alone had no effect on the nitrogen fluxes, but they did enhance the effect of copepods, possibly by influencing the quantity and quality of the copepods' excretion products. Our results show that small-scale biological interactions between bacteria, copepods and diatoms can have an important impact on denitrification and hence sediment nitrogen fluxes. PMID:25360602

Multiple Routes to Smart Nanostructured Materials from Diatom Microalgae: A Chemical Perspective.

PubMed

Ragni, Roberta; Cicco, Stefania R; Vona, Danilo; Farinola, Gianluca M

2018-05-01

Diatoms are unicellular photosynthetic microalgae, ubiquitously diffused in both marine and freshwater environments, which exist worldwide with more than 100 000 species, each with different morphologies and dimensions, but typically ranging from 10 to 200 µm. A special feature of diatoms is their production of siliceous micro- to nanoporous cell walls, the frustules, whose hierarchical organization of silica layers produces extraordinarily intricate pore patterns. Due to the high surface area, mechanical resistance, unique optical features, and biocompatibility, a number of applications of diatom frustules have been investigated in photonics, sensing, optoelectronics, biomedicine, and energy conversion and storage. Current progress in diatom-based nanotechnology relies primarily on the availability of various strategies to isolate frustules, retaining their morphological features, and modify their chemical composition for applications that are not restricted to those of the bare biosilica produced by diatoms. Chemical or biological methods that decorate, integrate, convert, or mimic diatoms' biosilica shells while preserving their structural features represent powerful tools in developing scalable, low-cost routes to a wide variety of nanostructured smart materials. Here, the different approaches to chemical modification as the basis for the description of applications relating to the different materials thus obtained are presented. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ocean acidification stimulates particulate organic carbon accumulation in two Antarctic diatom species under moderate and high natural solar radiation.

PubMed

Heiden, Jasmin P; Thoms, Silke; Bischof, Kai; Trimborn, Scarlett

2018-05-23

Impacts of rising atmospheric CO 2 concentrations and increased daily irradiances from enhanced surface water stratification on phytoplankton physiology in the coastal Southern Ocean remain still unclear. Therefore, in the two Antarctic diatoms Fragilariopsis curta and Odontella weissflogii the effects of moderate and high natural solar radiation combined with either ambient or future pCO 2 on cellular particulate organic carbon (POC) contents and photophysiology were investigated. Results showed that increasing CO 2 concentrations had greater impacts on diatom physiology than exposure to increasing solar radiation. Irrespective of the applied solar radiation regime, cellular POC quotas increased with future pCO 2 in both diatoms. Lowered maximum quantum yields of photochemistry in PSII (F v /F m ) indicated a higher photosensitivity under these conditions, being counteracted by increased cellular concentrations of functional photosynthetic reaction centers. Overall, our results suggest that both bloom-forming Antarctic coastal diatoms might increase carbon contents under future pCO 2 conditions despite reduced physiological fitness. This indicates a higher potential for primary productivity by the two diatom species with important implications for the CO 2 sequestration potential of diatom communities in the future coastal Southern Ocean. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Diatom paleoecology Pass Key core 37, Everglades National Park, Florida Bay

USGS Publications Warehouse

Pyle, Laura; Cooper, S.R.; Huvane, J.K.

1998-01-01

During the 20th century, there have been large-scale anthropogenic modifications to the South Florida ecosystem. The effects of these changes on Florida Bay and its biological communities are currently of political and scientific interest. This study is part of a larger effort to reconstruct the history of environmental changes in the bay, using paleoecological techniques. We are using diatom indicators preserved in Florida Bay sediments to infer long-term water quality, productivity, nutrient, and salinity changes. We are also obtaining information concerning the natural variability of the ecosystem. Diatoms are microscopic algae, the remains of which are generally well preserved in sediments, and their distributions are closely linked to water quality. Diatoms were extracted from a 70-cm sediment core collected from the Pass Key mudbank of Florida Bay by the U.S. Geological Survey. Between 300-500 diatom valves from each of 15 core samples were identified and counted. Estimates of absolute abundance, species richness, Shannon-Wiener diversity, and centric:pennate ratios were calculated for each sample that was counted. Information on the ecology of the diatom species is presented, and changes in diatom community composition are evaluated. Samples contained an average of four million diatom valves per gram of sediment. Major changes in the diatom community are evident down core. These include increases in the percent abundance of marine diatoms in the time period represented by the core, probably the result of increasing salinity at Pass Key. Benthic diatoms become less abundant in the top half of the core. This may be related to a number of factors including the die-off of sea grass beds or increased turbidity of the water column. Once the chronology of the Pass Key core 37 is established, these down-core changes can be related to historical events and compared with other indicators in the sedimentary record that are currently being investigated by U.S Geological Survey researchers. This report is preliminary and has not been reviewed for conformity with U.S. Geological Survey editorial standards or with the North American Stratigraphic Code. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Oxygen Isotope Calibration Study of Modern Diatoms in Freshwater Environments: Implications for Biogenic Silica as a Paleoclimate Proxy

NASA Astrophysics Data System (ADS)

Dodd, J. P.; Sharp, Z. D.; Fawcett, P.

2008-12-01

Oxygen isotope values of biogenic silica from diatom frustules are a commonly used proxy in freshwater and marine environments, and provide a valuable archive of paleoclimatic information such as temperature and water cycle processes. Advances in analytical techniques have made oxygen isotope measurements of diatom silica more robust; however, to date, there are multiple published fractionation factors for biogenic silica, with no general consensus on which is 'correct.' Previous studies (e.g. Moschen et al, 2005) demonstrated that there is no difference in SiO2-H2O fractionation between different size fractions of diatoms and, therefore, no species-dependent effects. The SiO2-H2O fractionation factors observed in laboratory grown diatoms analyzed by Brandriss et al. (1998) and modern lacustrine diatoms (Moschen et al., 2005) are in close agreement (τ = -0.2‰/°C) and are defined by the equations 1000lnα SiO2-H2O = 15.56 (103 T-1) - 20.92 and 1000lnα SiO2-H2O = 20.5 (103 T-1) - 36.2, respectively. However, these studies are not in agreement with other published SiO2-H2O fractionation factors for biogenic silica in marine and freshwater environments. In order to effectively utilize diatom δ18O values as a climate proxy, it is necessary to understand how oxygen isotopes are fractionated during silica frustule formation and identify potential errors in δ18O values obtained through different analytic/purification processes. Here we present oxygen isotope data from modern diatom species collected from a wide variety of natural riverine and lacustrine environments in northern New Mexico, USA. Temperatures at collection sites ranged from 5.5°C to 37.8°C. Preliminary isotope data indicate a SiO2-H2O fractionation factor identical to Brandriss et al. (1998). Additional experiments were undertaken to examine the effect of differing chemical purification techniques (i.e. HNO3, H2O2, and NaOH) on modern diatoms to see if processing techniques might affect the δ18O values of modern samples. Visual inspection of diatom frustules with a scanning electron microscope before and after treatment with HNO3 indicates no physical alteration of the frustule structure. To discount the possibility of oxygen exchange between diatom SiO2 and HNO3, samples were treated with an 18O-enriched nitric acid (1000‰), and the resulting δ18O values were essentially unchanged. Organic content following treatment with HNO3 was measured with an elemental analyzer and diatoms were considered to be pure SiO2 once weight percent carbon dropped below 0.01%. When diatoms were treated with H2O2 alone, significant organic material (>5 weight percent carbon) remained. Oxygen isotope values were obtained using a laser-extraction, stepwise fluorination technique that provides an additional visual confirmation of diatom purity. When pure F2 was introduced to the laser chamber during prefluorination, any sample with greater than 0.5 weight % carbon reacted violently to produce CF4 and O2 gas, and resulted in anomalous δ18O diatom values.

A Semianalytical Model for Pumping Tests in Finite Heterogeneous Confined Aquifers With Arbitrarily Shaped Boundary

NASA Astrophysics Data System (ADS)

Wang, Lei; Dai, Cheng; Xue, Liang

2018-04-01

This study presents a Laplace-transform-based boundary element method to model the groundwater flow in a heterogeneous confined finite aquifer with arbitrarily shaped boundaries. The boundary condition can be Dirichlet, Neumann or Robin-type. The derived solution is analytical since it is obtained through the Green's function method within the domain. However, the numerical approximation is required on the boundaries, which essentially renders it a semi-analytical solution. The proposed method can provide a general framework to derive solutions for zoned heterogeneous confined aquifers with arbitrarily shaped boundary. The requirement of the boundary element method presented here is that the Green function must exist for a specific PDE equation. In this study, the linear equations for the two-zone and three-zone confined aquifers with arbitrarily shaped boundary is established in Laplace space, and the solution can be obtained by using any linear solver. Stehfest inversion algorithm can be used to transform it back into time domain to obtain the transient solution. The presented solution is validated in the two-zone cases by reducing the arbitrarily shaped boundaries to circular ones and comparing it with the solution in Lin et al. (2016, https://doi.org/10.1016/j.jhydrol.2016.07.028). The effect of boundary shape and well location on dimensionless drawdown in two-zone aquifers is investigated. Finally the drawdown distribution in three-zone aquifers with arbitrarily shaped boundary for constant-rate tests (CRT) and flow rate distribution for constant-head tests (CHT) are analyzed.

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.

PubMed

Rimet, Frédéric; Chaumeil, Philippe; Keck, François; Kermarrec, Lenaïg; Vasselon, Valentin; Kahlert, Maria; Franc, Alain; Bouchez, Agnès

2016-01-01

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/. © The Author(s) 2016. Published by Oxford University Press.

Hydroecological Connections: Hyporheic Zone Weathering of Silicate Minerals Controls Diatom Biodiversity in Microbial Mats in Glacial Meltwater Streams of the McMurdo Dry Valleys, Antarctica

NASA Astrophysics Data System (ADS)

McKnight, D. M.; Dyson, I.; Esposito, R. M.; Gooseff, M. N.; Lyons, W. B.; Welch, K. A.

2015-12-01

The McMurdo Dry Valleys of Antarctica is comprised of alpine and terminal glaciers, large expanses of patterned ground, and ice-covered lakes in the valley floors, which are linked by glacial meltwater streams that flow during the austral summer. As part of the McMurdo Dry Valleys Long-Term Ecological research project, we have observed stream ecosystem response to a sustained 18 year cool period with low flows, which has been recently interrupted by three "flood events" during sunny, warm summers. Many of these streams contain thriving microbial mats comprised of cyanobacteria and endemic diatoms, the most diverse group of eukaryotic organisms in the valleys. Of the 45 diatom taxa, some common taxa are heavily silicified, Hantzschia amphioxys f. muelleri, while others are only lightly silicified. By comparing diatom communities in streams which flow every summer with those in streams that only flow during flood events, we found that hydrologic flow regime acts as a strong environmental filter on diatom community composition. Following the first flood event in 2001/02, mat biomass was two-fold lower due to scouring and recovered over several years, with lesser declines following the subsequent floods. In the longer streams, the diatom community composition remained stable through the flood events, whereas in two of the shorter streams, Green and Bowles Creeks, the diatom community shifted after the first flood event to a greater abundance of lightly silicified taxa. Water quality monitoring and reactive transport modeling have shown that rapid weathering of silicate minerals in the hyporheic zone accounts for the downstream increases in Si concentration which are observed in the longer streams. One mechanism driving this greater abundance of lightly silicified diatoms in shorter streams could be the greater dilution of the Si supply from hyporheic weathering in shorter streams under high flows. Given that the stream diatom community is well preserved in the 40,000-year sediment record from the receiving lake, greater understanding of hydrologic and biogeochemical controls on diatom community composition provides insight into the evolution of the lakes and geologic history of the region.

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

PubMed Central

Rimet, Frédéric; Chaumeil, Philippe; Keck, François; Kermarrec, Lenaïg; Vasselon, Valentin; Kahlert, Maria; Franc, Alain; Bouchez, Agnès

2016-01-01

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/ PMID:26989149

A synthesis of post-glacial diatom records from Lake Baikal

USGS Publications Warehouse

Bradbury, J. Platt; Bezrukova, E.; Chernyaeva, G.; Colman, S.M.; Khursevich, G.; King, J.W.; Likoshway, Ye. V.

1994-01-01

The biostratigraphy of fossil diatoms contributes important chronologic, paleolimnologic, and paleoclimatic information from Lake Baikal in southeastern Siberia. Diatoms are the dominant and best preserved microfossils in the sediments, and distinctive assemblages and species provide inter-core correlations throughout the basin at millennial to centennial scales, in both high and low sedimentation-rate environments. Distributions of unique species, once dated by radiocarbon, allow diatoms to be used as dating tools for the Holocene history of the lake.Diatom, pollen, and organic geochemical records from site 305, at the foot of the Selenga Delta, provide a history of paleolimnologic and paleoclimatic changes from the late glacial (15 ka) through the Holocene. Before 14 ka diatoms were very rare, probably because excessive turbidity from glacial meltwater entering the lake impeded productivity. Between 14 and 12 ka, lake productivity increased, perhaps as strong winds promoted deep mixing and nutrient regeneration. Pollen evidence suggests a cold shrub — steppe landscape dominated the central Baikal depression at this time. As summer insolation increased, conifers replaced steppe taxa, but diatom productivity declined between 11 and 9 ka perhaps as a result of increased summer turbidity resulting from violent storm runoff entering the lake via short, steep drainages. After 8 ka, drier, but more continental climates prevailed, and the modern diatom flora of Lake Baikal came to prominence.On Academician Ridge, a site of slow sedimentation rates, Holocene diatom assemblages at the top of 10-m cores reappear at deeper levels suggesting that such cores record at least two previous interglacial (or interstadial?) periods. Nevertheless, distinctive species that developed prior to the last glacial period indicate that the dynamics of nutrient cycling in Baikal and the responsible regional climatic environments were not entirely analogous to Holocene conditions. During glacial periods, the deep basin sediments of Lake Baikal are dominated by rapidly deposited clastics entering from large rivers with possibly glaciated headwaters. On the sublacustrine Academician Ridge (depth = 300 m), however, detailed analysis of the diatom biostratigraphy indicates that diastems (hiatuses of minor duration) and (or) highly variable rates of accumulation complicate paleolimnologic and paleoclimatic reconstructions from these records.

Identification of Highly Divergent Diatom-Derived Chloroplasts in Dinoflagellates, Including a Description of Durinskia kwazulunatalensis sp. nov. (Peridiniales, Dinophyceae).

PubMed

Yamada, Norico; Sym, Stuart D; Horiguchi, Takeo

2017-06-01

Dinoflagellates are known to possess chloroplasts of multiple origins derived from a red alga, a green alga, haptophytes, or diatoms. The monophyletic "dinotoms" harbor a chloroplast of diatom origin, but their chloroplasts are polyphyletic belonging to one of four genera: Chaetoceros, Cyclotella, Discostella, or Nitzschia. It has been speculated that serial replacement of diatom-derived chloroplasts by other diatoms has caused this diversity of chloroplasts. Although previous work suggested that the endosymbionts of Nitzschia origin might not be monophyletic, this has not been seriously investigated. To infer the number of replacements of diatom-derived chloroplasts in dinotoms, we analyzed the phylogenetic affinities of 14 species of dinotoms based on the endosymbiotic rbcL gene and SSU rDNA, and the host SSU rDNA. Resultant phylogenetic trees revealed that six species of Nitzschia were taken up by eight marine dinoflagellate species. Our phylogenies also indicate that four separate diatom species belonging to three genera were incorporated into the five freshwater dinotoms. Particular attention was paid to two crucially closely related species, Durinskia capensis and a novel species, D. kwazulunatalensis, because they possess distantly related Nitzschia species. This study clarified that any of a total of at least 11 diatom species in five genera are employed as an endosymbiont by 14 dinotoms, which infers a more frequent replacement of endosymbionts in the world of dinotoms than previously envisaged. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Distribution of Diatoms in Relation to Land Use and pH in Blackwater Coastal Plain Streams

NASA Astrophysics Data System (ADS)

Zampella, Robert A.; Laidig, Kim J.; Lowe, Rex L.

2007-03-01

We compared the composition of diatom assemblages collected from New Jersey Pinelands blackwater streams draining four different land uses, including forest land, abandoned-cranberry bogs, active-cranberry bogs, and developed and upland-agricultural land. Over a 2-year period (2002-2003), we collected 132 diatom taxa at 14 stream sites. Between-year variability in the composition of stream samples was high. Most diatom species were rarely encountered and were found in low abundance. Specific conductance and pH were higher at developed/agricultural sites compared with all other site types. Neither species richness nor genus richness was significantly different between stream types. However, clear community patterns were evident, and a significant difference in species composition existed between the developed/agricultural sites and both cranberry and forest sites. The primary community gradient, represented by the first axis of a DCA ordination, was associated with variations in pH and specific conductance. Although community patterns revealed by ordinating the data collected in 2002 differed from those obtained using the 2003 data, both ordinations contrasted the developed/agricultural sites and the other sites. Acidobiontic and acidophilous diatoms characterized the dominant species at forest, abandoned-bog, and cranberry sites, whereas indifferent species dominated the developed/agricultural samples. Although our study demonstrated a relationship between the composition of diatom assemblages and watershed conditions, several factors, including taxonomic problems, the large number of diatom species, incomplete pH classifications, and year-to-year variability may limit the utility of diatom species as indicators of watershed conditions in the New Jersey Pinelands.

Planktonic marine diatom record of the past 18 m.y.: Appearances and extinctions in the Pacific and Southern Oceans

USGS Publications Warehouse

Barron, J.A.

2003-01-01

Recently published diatom biochronologies provide accurate (to 0.1 m.y.) determination of the ages of appearances and disappearances of planktonic diatoms during the past 18 m.y. in the equatorial Pacific, North Pacific, and Southern Ocean. Comparisons of these records reveal the age of evolutionary appearance and extinction of species and their region of origin. Extinct planktonic diatom species have a mean longevity of 3.4 ?? 2.8 m.y. (SD, n = 53) in the equatorial Pacific, 2.5 ?? 2.1 m.y. (n = 52) in the North Pacific, and 2.9 ?? 2.3 m.y. (n = 38) in the Southern Ocean. The relatively large standard deviations are likely due to the inclusion of taxa that probably could be subdivided into two or more species. In the equatorial Pacific, evolutionary turnover of diatom species was relatively high between 18.0 and 6.0 Ma compared with the period after 6.0 Ma, presumably reflecting changing oceanic circulation and evolving water masses. In the North Pacific, evolutionary turnover peaked between 10.0 and 4.5 Ma, with increasing high-latitude cooling and enhanced provincialism. In the Southern Ocean, evolutionary turnover of endemic diatoms was greatest between 5.0 and 1.6 Ma, which provides evidence for the strong provincial character of Pliocene diatom assemblages. Taken as a whole, oceanic diatom assemblages became increasingly provincial in character during the late Miocene and Pliocene, as pole-to-equator thermal gradients increased and oceanic frontal systems were strengthened.

Insights into global diatom distribution and diversity in the world's ocean.

PubMed

Malviya, Shruti; Scalco, Eleonora; Audic, Stéphane; Vincent, Flora; Veluchamy, Alaguraj; Poulain, Julie; Wincker, Patrick; Iudicone, Daniele; de Vargas, Colomban; Bittner, Lucie; Zingone, Adriana; Bowler, Chris

2016-03-15

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.

Insights into global diatom distribution and diversity in the world’s ocean

PubMed Central

Malviya, Shruti; Scalco, Eleonora; Audic, Stéphane; Vincent, Flora; Veluchamy, Alaguraj; Poulain, Julie; Wincker, Patrick; Iudicone, Daniele; de Vargas, Colomban; Bittner, Lucie; Zingone, Adriana; Bowler, Chris

2016-01-01

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered. PMID:26929361

Heterologous co-expression of a yeast diacylglycerol acyltransferase (ScDGA1) and a plant oleosin (AtOLEO3) as an efficient tool for enhancing triacylglycerol accumulation in the marine diatom Phaeodactylum tricornutum.

PubMed

Zulu, Nodumo Nokulunga; Popko, Jennifer; Zienkiewicz, Krzysztof; Tarazona, Pablo; Herrfurth, Cornelia; Feussner, Ivo

2017-01-01

Microalgae are promising alternate and renewable sources for producing valuable products such as biofuel and essential fatty acids. Although this is the case, there are still challenges impeding on the effective commercial production of microalgal products. For instance, their product yield is still too low. Therefore, this study was oriented towards enhancing triacylglycerol (TAG) accumulation in the diatom Phaeodactylum tricornutum (strain Pt4). To achieve this, a type 2 acyl-CoA:diacylglycerol acyltransferase from yeast ( ScDGA1 ) and the lipid droplet (LD) stabilizing oleosin protein 3 from Arabidopsis thaliana ( AtOLEO3 ) were expressed in Pt4. The individual expression of ScDGA1 and AtOLEO3 in Pt4 resulted in a 2.3- and 1.4-fold increase in TAG levels, respectively, in comparison to the wild type. The co-expression of both, ScDGA1 and AtOLEO3 , was accompanied by a 3.6-fold increase in TAG content. On the cellular level, the lines co-expressing ScDGA1 and AtOLEO3 showed the presence of the larger and increased numbers of lipid droplets when compared to transformants expressing single genes and an empty vector. Under nitrogen stress, TAG productivity was further increased twofold in comparison to nitrogen-replete conditions. While TAG accumulation was enhanced in the analyzed transformants, the fatty acid composition remained unchanged neither in the total lipid nor in the TAG profile. The co-expression of two genes was shown to be a more effective strategy for enhancing TAG accumulation in P. tricornutum strain Pt4 than a single gene strategy. For the first time in a diatom, a LD protein from a vascular plant, oleosin, was shown to have an impact on TAG accumulation and on LD organization.

Simbrain 3.0: A flexible, visually-oriented neural network simulator.

PubMed

Tosi, Zachary; Yoshimi, Jeffrey

2016-11-01

Simbrain 3.0 is a software package for neural network design and analysis, which emphasizes flexibility (arbitrarily complex networks can be built using a suite of basic components) and a visually rich, intuitive interface. These features support both students and professionals. Students can study all of the major classes of neural networks in a familiar graphical setting, and can easily modify simulations, experimenting with networks and immediately seeing the results of their interventions. With the 3.0 release, Simbrain supports models on the order of thousands of neurons and a million synapses. This allows the same features that support education to support research professionals, who can now use the tool to quickly design, run, and analyze the behavior of large, highly customizable simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

The viscoelastic behavior of a composite in a thermal environment

NASA Technical Reports Server (NTRS)

Morris, D. H.; Brinson, H. F.; Griffith, W. I.; Yeow, Y. T.

1979-01-01

A proposed method for the accelerated predictions of modulus and life times for time dependent polymer matrix composite laminates is presented. The method, based on the time temperature superposition principle and lamination theory, is described in detail. Unidirectional reciprocal of compliance master curves and the shift functions needed are presented and discussed. Master curves for arbitrarily oriented unidirectional laminates are predicted and compared with experimantal results obtained from master curves generated from 15 minute tests and with 25 hour tests. Good agreement is shown. Predicted 30 deg and 60 deg unidirectional strength master curves are presented and compared to results of creep rupture tests. Reasonable agreement is demonstrated. In addition, creep rupture results for a (90 deg + or - 60 deg/90 deg) sub 2s laminate are presented.

Method for determining artillery position

NASA Technical Reports Server (NTRS)

Fischer, Johannes; Loges, Werner; Meuser, Wilfried

1988-01-01

A method is disclosed for determining the position of cannon from measurement sites whose distance from each other lies in the same order of magnitude as the distance between the cannons -- that distance being in the kilometer range -- with the help of the travel time evaluation of muzzle blasts received at the measurement sites. There are at least two measurement sites, consisting of a cruciform of four microphones each positioned so that one axis is oriented to an arbitrarily chosen reference direction with the microphones spaced closely together. In this arrangement of diametrically opposed microphones, the respective travel times are determined and placed in a relationship whose arctangent is a radio bearing to the reference direction in which radio bearings are determined with consideration of their position and their opposing distance from the cannon position.

Numerical and experimental investigation of light trapping effect of nanostructured diatom frustules

NASA Astrophysics Data System (ADS)

Chen, Xiangfan; Wang, Chen; Baker, Evan; Sun, Cheng

2015-07-01

Recent advances in nanophotonic light-trapping technologies offer promising solutions in developing high-efficiency thin-film solar cells. However, the cost-effective scalable manufacturing of those rationally designed nanophotonic structures remains a critical challenge. In contrast, diatoms, the most common type of phytoplankton found in nature, may offer a very attractive solution. Diatoms exhibit high solar energy harvesting efficiency due to their frustules (i.e., hard porous cell wall made of silica) possessing remarkable hierarchical micro-/nano-scaled features optimized for the photosynthetic process through millions of years of evolution. Here we report numerical and experimental studies to investigate the light-trapping characteristic of diatom frustule. Rigorous coupled wave analysis (RCWA) and finite-difference time-domain (FDTD) methods are employed to investigate the light-trapping characteristics of the diatom frustules. In simulation, placing the diatom frustules on the surface of the light-absorption materials is found to strongly enhance the optical absorption over the visible spectrum. The absorption spectra are also measured experimentally and the results are in good agreement with numerical simulations.

Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment.

PubMed

Rosenwasser, Shilo; Graff van Creveld, Shiri; Schatz, Daniella; Malitsky, Sergey; Tzfadia, Oren; Aharoni, Asaph; Levin, Yishai; Gabashvili, Alexandra; Feldmesser, Ester; Vardi, Assaf

2014-02-18

Diatoms are ubiquitous marine photosynthetic eukaryotes responsible for approximately 20% of global photosynthesis. Little is known about the redox-based mechanisms that mediate diatom sensing and acclimation to environmental stress. Here we used a quantitative mass spectrometry-based approach to elucidate the redox-sensitive signaling network (redoxome) mediating the response of diatoms to oxidative stress. We quantified the degree of oxidation of 3,845 cysteines in the Phaeodactylum tricornutum proteome and identified approximately 300 redox-sensitive proteins. Intriguingly, we found redox-sensitive thiols in numerous enzymes composing the nitrogen assimilation pathway and the recently discovered diatom urea cycle. In agreement with this finding, the flux from nitrate into glutamine and glutamate, measured by the incorporation of (15)N, was strongly inhibited under oxidative stress conditions. Furthermore, by targeting the redox-sensitive GFP sensor to various subcellular localizations, we mapped organelle-specific oxidation patterns in response to variations in nitrogen quota and quality. We propose that redox regulation of nitrogen metabolism allows rapid metabolic plasticity to ensure cellular homeostasis, and thus is essential for the ecological success of diatoms in the marine ecosystem.

Extremophile Diatoms: Implications to the Drake Equation

NASA Technical Reports Server (NTRS)

Sterrenburg, Frithjof A. S.; Hoover, Richard B.

2011-01-01

Diatoms are unicellular Eukaryotes that (as a group and phylogenetically) are not strictly regarded as extremophiles , since the vast majority of diatoms are mesophilic photoautotrophs. However, among the terrestrial Eukaryotes, diatoms are by far the single group of organisms with the ability to inhabit the greatest range of hostile environments on Earth. They are the dominant eukaryotes in the polar regions; in fumaroles, hot springs and geysers; and in hypersaline and hyperalkaline lakes and pools. Cryophilic species such as Fragilaria sublinearis and Chaetoceras fragilis are able to carry out respiration at extremely low rates at low temperatures in darkness. The Drake Equation refers to the likelihood of there being intelligent life at the technological level of electromagnetic communication. However, consideration of the range of conditions suitable for the habitability of eukaryotic diatoms and prokaryotic extremophiles, the likelihood that life exists elsewhere in the cosmos becomes many orders of magnitude greater than that predicted by the classical Drake Equation. In this paper we review the characteristics of diatoms as eukaryotic extremophiles and consider the implications to adjustments needed to the Drake Equation to assess the possibility that life exists elsewhere in the Universe.

Inland diatoms from the McMurdo Dry Valleys and James Ross Island, Antarctica

USGS Publications Warehouse

Esposito, R.M.M.; Spaulding, S.A.; McKnight, Diane M.; Van De Vijver, B.; Kopalova, K.; Lubinski, D.; Hall, B.; Whittaker, T.

2008-01-01

Diatom taxa present in the inland streams and lakes of the McMurdo Dry Valleys and James Ross Island, Antarctica, are presented in this paper. A total of nine taxa are illustrated, with descriptions of four new species (Luticola austroatlantica sp. nov., Luticola dolia sp. nov., Luticola laeta sp. nov., Muelleria supra sp. nov.). In the perennially ice-covered lakes of the McMurdo Dry Valleys, diatoms are confined to benthic mats within the photic zone. In streams, diatoms are attached to benthic surfaces and within the microbial mat matrix. One species, L. austroatlantica, is found on James Ross Island, of the southern Atlantic archipelago, and the McMurdo Dry Valleys. The McMurdo Dry Valley populations are at the lower range of the size spectrum for the species. Streams flow for 6-10 weeks during the austral summer, when temperatures and solar radiation allow glacial ice to melt. The diatom flora of the region is characterized by species assemblages favored under harsh conditions, with naviculoid taxa as the dominant group and several major diatom groups conspicuously absent. ?? 2008 NRC.

Frustules to fragments, diatoms to dust: How degradation of microfossil shape and microstructures can teach us how ice sheets work

USGS Publications Warehouse

Scherer, R.P.; Sjunneskog, C.M.; Iverson, M.R.; Hooyer, T.S.

2005-01-01

In a laboratory experiment we investigated micro- and nanoscale changes in fossil diatom valves and in the texture of diatomaceous sediments that result from ice sheet overburden and subglacial shearing. Our experiment included compression and shearing of Antarctic diatom-rich sediments in a ring shear device and comparison of experimental samples with natural glacial sediments from the Antarctic continental shelf. The purpose of the experiment is to establish objective criteria for analyzing subglacial processes and interpreting the origin of glacial-geologic features on the Antarctic continental shelf. We find distinct changes resulting from different glacial settings, with respect to whole diatom frustules, diatom micromorphology, and microtextural properties of sedimentary units. By providing constraints on subglacial shearing, these observations of genetically controlled micro- and nanoscale diatom structures and architecture are contributing to the understanding of large-scale glacial processes, aiding the development of models of modern ice sheet processes, and guiding interpretation of past ice sheet configurations. Copyright ?? 2005 American Scientific Publishers. All rights reserved.

Decadal variations in diatoms and dinoflagellates on the inner shelf of the East China Sea, China

NASA Astrophysics Data System (ADS)

Abate, Rediat; Gao, Yahui; Chen, Changping; Liang, Junrong; Mu, Wenhua; Kifile, Demeke; Chen, Yanghang

2017-11-01

Diatoms and dinoflagellates are two major groups of phytoplankton that flourish in the oceans, particularly in coastal zone and upwelling systems, and their contrasting production have been reported in several world seas. However, this information is not available in the coastal East China Sea (ECS). Thus, to investigate and compare the decadal trends in diatoms and dinoflagellates, a sediment core, 47 cm long, was collected from the coastal zone of the ECS. Sediment chlorophyll- a (Chl- a), phytoplankton-group specific pigment signatures of diatoms and dinoflagellates, and diatom valve concentrations were determined. The sediment core covered the period from 1961 to 2011 AD. The chlorophyll- a contents ranged from 2.32 to 73 µg/g dry sediment (dw) and averaged 9.81 µg/g dw. Diatom absolute abundance ranged from 29152 to 177501 valve/gram (v/g) dw and averaged 72137 v/g dw. Diatom valve and diatom specific pigment marker concentrations were not significantly correlated. Peridinin increased after the 1980s in line with intensified use of fertilizer and related increases in nutrient inputs into the marine environment. The increased occurrence of dinoflagellate dominance after the 1980s can be mostly explained by the increase in nutrients. However, the contribution of dinoflagellates to total phytoplankton production (Chl- a) decreased during the final decade of this study, probably because of the overwhelming increase in diatom production that corresponded with the construction of the Three Gorges Dam (TGD) and related light availability. Similarly, the mean ratio of fucoxanthin/peridinin for the period from 1982 to 2001 was 6% less than for 1961 to 1982, while the ratio for 2001 to 2011 was 45.3% greater than for 1982 to 2001. The decadal variation in the fucoxanthin/peridinin ratio implies that dinoflagellate production had been gradually increasing until 2001. We suggest that the observed changes can be explained by anthropogenic impacts, such as nutrient loading and dam construction.

Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms

PubMed Central

Groussman, Ryan D.; Parker, Micaela S.; Armbrust, E. Virginia

2015-01-01

Ferroproteins arose early in Earth’s history, prior to the emergence of oxygenic photosynthesis and the subsequent reduction of bioavailable iron. Today, iron availability limits primary productivity in about 30% of the world’s oceans. Diatoms, responsible for nearly half of oceanic primary production, have evolved molecular strategies for coping with variable iron concentrations. Our understanding of the evolutionary breadth of these strategies has been restricted by the limited number of species for which molecular sequence data is available. To uncover the diversity of strategies marine diatoms employ to meet cellular iron demands, we analyzed 367 newly released marine microbial eukaryotic transcriptomes, which include 47 diatom species. We focused on genes encoding proteins previously identified as having a role in iron management: iron uptake (high-affinity ferric reductase, multi-copper oxidase, and Fe(III) permease); iron storage (ferritin); iron-induced protein substitutions (flavodoxin/ferredoxin, and plastocyanin/cytochrome c6) and defense against reactive oxygen species (superoxide dismutases). Homologs encoding the high-affinity iron uptake system components were detected across the four diatom Classes suggesting an ancient origin for this pathway. Ferritin transcripts were also detected in all Classes, revealing a more widespread utilization of ferritin throughout diatoms than previously recognized. Flavodoxin and plastocyanin transcripts indicate possible alternative redox metal strategies. Predicted localization signals for ferredoxin identify multiple examples of gene transfer from the plastid to the nuclear genome. Transcripts encoding four superoxide dismutase metalloforms were detected, including a putative nickel-coordinating isozyme. Taken together, our results suggest that the majority of iron metabolism genes in diatoms appear to be vertically inherited with functional diversity achieved via possible neofunctionalization of paralogs. This refined view of iron use strategies in diatoms elucidates the history of these adaptations, and provides potential molecular markers for determining the iron nutritional status of different diatom species in environmental samples. PMID:26052941

An experiment to assess the effects of diatom dissolution on oxygen isotope ratios.

PubMed

Smith, Andrew C; Leng, Melanie J; Swann, George E A; Barker, Philip A; Mackay, Anson W; Ryves, David B; Sloane, Hilary J; Chenery, Simon R N; Hems, Mike

2016-01-30

Current studies which use the oxygen isotope composition from diatom silica (δ(18) Odiatom ) as a palaeoclimate proxy assume that the δ(18) Odiatom value reflects the isotopic composition of the water in which the diatom formed. However, diatoms dissolve post mortem, preferentially losing less silicified structures in the water column and during/after burial into sediments. The impact of dissolution on δ(18) Odiatom values and potential misinterpretation of the palaeoclimate record are evaluated. Diatom frustules covering a range of ages (6 samples from the Miocene to the Holocene), environments and species were exposed to a weak alkaline solution for 48 days at two temperatures (20 °C and 4 °C), mimicking natural dissolution post mucilage removal. Following treatment, dissolution was assessed using scanning electron microscope images and a qualitative diatom dissolution index. The diatoms were subsequently analysed for their δ(18) O values using step-wise fluorination and isotope ratio mass spectrometry. Variable levels of diatom dissolution were observed between the six samples; in all cases higher temperatures resulted in more frustule degradation. Dissolution was most evident in younger samples, probably as a result of the more porous nature of the silica. The degree of diatom dissolution does not directly equate to changes in the isotope ratios; the δ(18) Odiatom value was, however, lower after dissolution, but in only half the samples was this reduction outside the analytical error (2σ analytical error = 0.46‰). We have shown that dissolution can have a small negative impact on δ(18) Odiatom values, causing reductions of up to 0.59‰ beyond analytical error (0.46‰) at natural environmental temperatures. These findings need to be considered in palaeoenvironmental reconstructions using δ(18) Odiatom values, especially when interpreting variations in these values of <1‰. Copyright © 2015 John Wiley & Sons, Ltd.

Evolutionary origins and functions of the carotenoid biosynthetic pathway in marine diatoms.

PubMed

Coesel, Sacha; Oborník, Miroslav; Varela, Joao; Falciatore, Angela; Bowler, Chris

2008-08-06

Carotenoids are produced by all photosynthetic organisms, where they play essential roles in light harvesting and photoprotection. The carotenoid biosynthetic pathway of diatoms is largely unstudied, but is of particular interest because these organisms have a very different evolutionary history with respect to the Plantae and are thought to be derived from an ancient secondary endosymbiosis between heterotrophic and autotrophic eukaryotes. Furthermore, diatoms have an additional xanthophyll-based cycle for dissipating excess light energy with respect to green algae and higher plants. To explore the origins and functions of the carotenoid pathway in diatoms we searched for genes encoding pathway components in the recently completed genome sequences of two marine diatoms. Consistent with the supplemental xanthophyll cycle in diatoms, we found more copies of the genes encoding violaxanthin de-epoxidase (VDE) and zeaxanthin epoxidase (ZEP) enzymes compared with other photosynthetic eukaryotes. However, the similarity of these enzymes with those of higher plants indicates that they had very probably diversified before the secondary endosymbiosis had occurred, implying that VDE and ZEP represent early eukaryotic innovations in the Plantae. Consequently, the diatom chromist lineage likely obtained all paralogues of ZEP and VDE genes during the process of secondary endosymbiosis by gene transfer from the nucleus of the algal endosymbiont to the host nucleus. Furthermore, the presence of a ZEP gene in Tetrahymena thermophila provides the first evidence for a secondary plastid gene encoded in a heterotrophic ciliate, providing support for the chromalveolate hypothesis. Protein domain structures and expression analyses in the pennate diatom Phaeodactylum tricornutum indicate diverse roles for the different ZEP and VDE isoforms and demonstrate that they are differentially regulated by light. These studies therefore reveal the ancient origins of several components of the carotenoid biosynthesis pathway in photosynthetic eukaryotes and provide information about how they have diversified and acquired new functions in the diatoms.

Phase retrieval with the transport-of-intensity equation in an arbitrarily-shaped aperture by iterative discrete cosine transforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Lei; Zuo, Chao; Idir, Mourad

A novel transport-of-intensity equation (TIE) based phase retrieval method is proposed with putting an arbitrarily-shaped aperture into the optical wavefield. In this arbitrarily-shaped aperture, the TIE can be solved under non-uniform illuminations and even non-homogeneous boundary conditions by iterative discrete cosine transforms with a phase compensation mechanism. Simulation with arbitrary phase, arbitrary aperture shape, and non-uniform intensity distribution verifies the effective compensation and high accuracy of the proposed method. Experiment is also carried out to check the feasibility of the proposed method in real measurement. Comparing to the existing methods, the proposed method is applicable for any types of phasemore » distribution under non-uniform illumination and non-homogeneous boundary conditions within an arbitrarily-shaped aperture, which enables the technique of TIE with hard aperture become a more flexible phase retrieval tool in practical measurements.« less

Phase retrieval with the transport-of-intensity equation in an arbitrarily-shaped aperture by iterative discrete cosine transforms

DOE PAGES

Huang, Lei; Zuo, Chao; Idir, Mourad; ...

2015-04-21

A novel transport-of-intensity equation (TIE) based phase retrieval method is proposed with putting an arbitrarily-shaped aperture into the optical wavefield. In this arbitrarily-shaped aperture, the TIE can be solved under non-uniform illuminations and even non-homogeneous boundary conditions by iterative discrete cosine transforms with a phase compensation mechanism. Simulation with arbitrary phase, arbitrary aperture shape, and non-uniform intensity distribution verifies the effective compensation and high accuracy of the proposed method. Experiment is also carried out to check the feasibility of the proposed method in real measurement. Comparing to the existing methods, the proposed method is applicable for any types of phasemore » distribution under non-uniform illumination and non-homogeneous boundary conditions within an arbitrarily-shaped aperture, which enables the technique of TIE with hard aperture become a more flexible phase retrieval tool in practical measurements.« less

Shift in the species composition of the diatom community in the eutrophic Mauritanian coastal upwelling: Results from a multi-year sediment trap experiment (2003-2010)

NASA Astrophysics Data System (ADS)

Romero, Oscar E.; Fischer, Gerhard

2017-12-01

A multiannual, continuous sediment trap experiment was conducted at the mooring site CBeu (Cape Blanc eutrophic, ca. 20 °N, ca. 18 °W; trap depth = 1256-1296 m) in the high-productive Mauritanian coastal upwelling. Here we present fluxes and the species-specific composition of the diatom assemblage, and fluxes of biogenic silica (BSi, opal) and total organic carbon (TOC) for the time interval June 2003-Feb 2010. Flux ranges of studied parameters are (i) total diatoms = 1.2 ∗ 108-4.7 ∗ 104 valves m-2 d-1 (average = 5.9 × 106 valves ± 1.4 × 107); (ii) BSi = 296-0.5 mg m-2 d-1 (average = 41.1 ± 53.5 mg m-2 d-1), and (iii) TOC = 97-1 mg m-2 d-1 (average = 20.5 ± 17.8 mg m-2 d-1). Throughout the experiment, the overall good match of total diatom, BSi and TOC fluxes is reasonably consistent and reflects well the temporal occurrence of the main Mauritanian upwelling season. Spring and summer are the most favorable seasons for diatom production and sedimentation: out of the recorded 14 diatom maxima of different magnitude, six occurred in spring and four in summer. The diverse diatom community at site CBeu is composed of four main assemblages: benthic, coastal upwelling, coastal planktonic and open-ocean diatoms, reflecting different productivity conditions and water masses. A striking feature of the temporal variability of the diatom populations is the persistent pattern of seasonal groups' contribution: benthic and coastal upwelling taxa dominated during the main upwelling season in spring, while open-ocean diatoms were more abundant in fall and winter, when the upper water column becomes stratified, upwelling relaxes and productivity decreases. The relative abundance of benthic diatoms strongly increased after 2006, yet their spring-summer contribution remained high until the end of the trap experiment. The occurrence of large populations of benthic diatoms at the hemipelagic CBeu site is interpreted to indicate transport from shallow waters via nepheloid layers. We argue that a significant amount of valves, BSi and TOC produced in waters overlying the Banc d'Arguin and the Mauritanian shelf is effectively transported to the CBeu trap in intermediate waters at the outer Mauritanian slope. The impact of the intermediate and bottom-near nepheloid layers-driven transport in the transfer of valves and bulk particulates and its potential contribution to the export of biogenic materials from the shelf and uppermost slope might play a significant role in hemipelagial fluxes off Mauritania.

Water quality (2000-08) and historical phosphorus concentrations from paleolimnological studies of Swamp and Speckled Trout Lakes, Grand Portage Reservation, northeastern Minnesota

USGS Publications Warehouse

Christensen, Victoria G.; Jones, Perry M.; Edlund, Mark B.; Ramstack, Joy M.

2010-01-01

A paleolimnological approach was taken to aid the Grand Portage Reservation, in northeastern Minnesota, in determining reference conditions for lakes on the reservation. The U.S. Geological Survey, in cooperation with the Grand Portage Band of Chippewa Indians and the Science Museum of Minnesota, conducted a study to describe water quality (2000-08) and historical total phosphorus concentrations (approximately 1781-2006) for Swamp and Speckled Trout Lakes. Results from this study may be used as a guide in establishing nutrient criteria in these and other lakes on the Grand Portage Reservation. Historical phosphorus concentrations were inferred through paleolimnological reconstruction methods involving diatom analysis and lead-210 dating of lake-sediment cores. Historical diatom-inferred total phosphorus concentrations in Swamp Lake ranged from 0.017 to 0.025 milligrams per liter (mg/L) based on diatom assemblages in sediment samples dated 1781-2005. Historical diatom-inferred total phosphorus concentrations in Speckled Trout Lake ranged from 0.008 to 0.014 mg/L based on diatom assemblages in sediment samples dated 1825-2006. In both lakes, historical changes in diatom-inferred total phosphorus concentrations did not exceed model error estimates, indicating that there has been minimal change in total phosphorus concentrations in the two lakes over about two centuries. Nutrient concentrations in monthly water samples collected May through October during 2000, 2002, 2004, 2006, and 2008 were compared to the diatom-inferred total phosphorus concentrations. Total phosphorus concentrations from water samples collected from Swamp Lake during 2000-08 ranged from less than 0.002 to 0.160 mg/L (median= 0.023 mg/L) compared to diatom-inferred total phosphorus concentrations of 0.018 to 0.020 mg/L for 2002 to 2005. Total phosphorus concentrations in water samples collected from Speckled Trout Lake during 2000-08 were similar to those of Swamp Lake, ranging from less than 0.002 to 0.147 mg/L (median=0.012 mg/L), whereas the diatom-inferred total phosphorus concentrations were smaller, ranging from 0.009 to 0.010 mg/L for 2003 to 2006. Differences in total phosphorus concentrations between the two lakes may be because of differences in watershed characteristics, particularly the number of wetlands in the two watersheds. Similarities between recent total phosphorus concentrations in water-quality samples and diatom-inferred total phosphorus indicate that diatom-inferred phosphorus reconstructions might be used to help establish reference conditions. Nutrient criteria for Grand Portage Reservation lakes may be established when a sampling program is designed to ensure representative phosphorus concentrations in water samples are comparable to diatom-inferred concentrations.

Photoluminescence detection of 2,4,6-trinitrotoluene (TNT) binding on diatom frustule biosilica functionalized with an anti-TNT monoclonal antibody fragment.

PubMed

Zhen, Le; Ford, Nicole; Gale, Debra K; Roesijadi, Guritno; Rorrer, Gregory L

2016-05-15

A selective and label-free biosensor for detection of the explosive compound 2,4,6-trinitrotoluene (TNT) in aqueous solution was developed based on the principle of photoluminescence quenching of upon immunocomplex formation with antibody-functionalized diatom frustule biosilica. The diatom frustule is an intricately nanostructured, highly porous biogenic silica material derived from the shells of microscopic algae called diatoms. This material emits strong visible blue photoluminescence (PL) upon UV excitation. PL-active frustule biosilica was isolated from cultured cells of the marine diatom Pinnularia sp. and functionalized with a single chain variable fragment (scFv) derived from an anti-TNT monoclonal antibody. When TNT was bound to the anti-TNT scFv-functionalized diatom frustule biosilica, the PL emission from the biosilica was partially quenched due to the electrophilic nature of the nitro (-NO2) groups on the TNT molecule. The dose-response curve for immunocomplex formation of TNT on the scFv-functionalized diatom frustule biosilica had a half-saturation binding constant of 6.4 ± 2.4·10(-8)M and statistically-significant measured detection limit of 3.5·10(-8)M. The binding and detection were selective for TNT and TNB (trinitrobenzene) but not RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) or 2,6-DNT (2,6-dinitrotoluene). Copyright © 2016. Published by Elsevier B.V.

Some aspects of water quality in a polluted lowland river in relation to the intracellular chemical levels in planktonic and epilithic diatoms.

PubMed

Tien, Chien-Jung

2004-04-01

Changes in elemental concentrations of diatoms and river water from the river Erh-Jen were determined using scanning electron microscopy energy-dispersive X-ray microanalysis and inductively coupled plasma mass spectrometry. Relatively large amounts of copper and lead found in both planktonic and epilithic diatoms implied these algae might play an important role in biogeochemical cycles and in the transfer of those elements to higher trophic levels in the aquatic environment. Changes in elemental concentrations within diatom cells were found to vary with other elements within cells and the same or different elements in water. Planktonic and epilithic cells showed different correlation patterns. For epilithic diatoms, negative correlations were found between concentrations of total phosphorus and phosphate in water and those of phosphorus within cells, and between concentrations of lead in water and in cells. Concentrations of chromium and mercury within planktonic cells and those of phosphorus, manganese and lead within epilithic ones were found to be easily influenced by other elements in river water, indicating appearance of the competitive manner on uptake of such elements by algal cells. Relatively high concentration factors (CFs) for cadmium, mercury and lead by diatoms in this study suggested they are good accumulators for these heavy metals. Significant negative corrections were found between the CFs of diatoms and the concentrations of elements in river water.

Diatom cultivation and biotechnologically relevant products. Part II: current and putative products.

PubMed

Lebeau, T; Robert, J-M

2003-02-01

While diatoms are widely present in terms of diversity and abundance in nature, few species are currently used for biotechnologically applications. Most studies have focussed on intracellularly synthesised eicosapentaenoic acid (EPA), a polyunsaturated fatty acid (PUFA) used for pharmaceutical applications. Applications for other intracellular molecules, such as total lipids for biodiesel, amino acids for cosmetic, antibiotics and antiproliferative agents, are at the early stage of development. In addition, the active principle component must be identified amongst the many compounds of biotechnological interest. Biomass from diatom culture may be applied to: (1). aquaculture diets, due to the lipid- and amino-acid-rich cell contents of these microorganisms, and (2). the treatment of water contaminated by phosphorus and nitrogen in aquaculture effluent, or heavy metal (bioremediation). The most original application of microalgal biomass, and specifically diatoms, is the use of silicon derived from frustules in nanotechnology. The competitiveness of biotechnologically relevant products from diatoms will depend on their cost of production. Apart from EPA, which is less expensive when obtained from Phaeodactylum tricornutum than from cod liver, comparative economic studies of other diatom-derived products as well as optimisation of culture conditions are needed. Extraction of intracellular metabolites should be also optimised to reduce production costs, as has already been shown for EPA. Using cell immobilisation techniques, benthic diatoms can be cultivated more efficiently allowing new, biotechnologically relevant products to be investigated.

Diatom silica microparticles for sustained release and permeation enhancement following oral delivery of prednisone and mesalamine.

PubMed

Zhang, Hongbo; Shahbazi, Mohammad-Ali; Mäkilä, Ermei M; da Silva, Tiago H; Reis, Rui L; Salonen, Jarno J; Hirvonen, Jouni T; Santos, Hélder A

2013-12-01

Diatoms are porous silica-based materials obtained from single cell photosynthetic algae. Despite low cost, easy purification process, environmentally safe properties, and rapidly increasing potentials for medical applications, the cytotoxicity of diatoms and the effect on drug permeation of oral formulations have not been studied so far. Herein, we have evaluated the potential of diatom silica microparticles (DSMs) for the delivery of mesalamine and prednisone, which are two commonly prescribed drugs for gastrointestinal (GI) diseases. Transmission electron microscopy analysis of the morphological surface changes of Caco-2/HT-29 monolayers and the cell viability data in colon cancer cells (Caco-2, HT-29 and HCT-116) showed very low toxicity of diatoms at concentrations up to 1000 μg/mL. The mesalamine and prednisone release under simulated GI conditions indicated prolonged release of both drugs from the diatoms. Furthermore, drug permeation across Caco-2/HT-29 co-culture monolayers demonstrated that diatoms are capable to enhance the drug permeability. Overall, this study evaluated DSMs' cytotoxicity in colon cancer cells and the effect of DSMs on drug permeability across Caco-2/HT-29 monolayers. Our results demonstrate that DSMs can be considered as a non-cytotoxic biomaterial with high potential to improve the mesalamine and prednisone bioavailability by sustaining the drug release and enhancing drug permeability. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dynamic sinking behaviour in marine phytoplankton: rapid changes in buoyancy may aid in nutrient uptake.

PubMed

Gemmell, Brad J; Oh, Genesok; Buskey, Edward J; Villareal, Tracy A

2016-10-12

Phytoplankton sinking is an important property that can determine community composition in the photic zone and material loss to the deep ocean. To date, studies of diatom suspension have relied on bulk measurements with assumptions that bulk rates adequately capture the essential characteristics of diatom sinking. However, recent work has illustrated that individual diatom sinking rates vary considerably from the mean bulk rate. In this study, we apply high-resolution optical techniques, individual-based observations of diatom sinking and a recently developed method of flow visualization around freely sinking cells. The results show that in both field samples and laboratory cultures, some large species of centric diatoms are capable of a novel behaviour, whereby cells undergo bursts of rapid sinking that alternate with near-zero sinking rates on the timescales of seconds. We also demonstrate that this behaviour is under direct metabolic control of the cell. We discuss these results in the context of implications for nutrient flux to the cell surface. While nutrient flux in large diatoms increases during fast sinking, current mass transport models cannot incorporate the unsteady sinking behaviour observed in this study. However, large diatoms appear capable of benefiting from the enhanced nutrient flux to their surface during rapid sinking even during brief intervening periods of near-zero sinking rates. © 2016 The Author(s).

Contrasting morphological and DNA barcoding methods for diatom (Bacillariophyta) identification from environmental samples in the Eightmile River in Connecticut U.S.A.

USDA-ARS?s Scientific Manuscript database

The dominant and traditional approach used to identify diatom species is morphological characterization with light (LM) and scanning electron microscopy (SEM). However, using morphology alone to distinguish diatom species can be challenging because the phenotype of a species is often influenced by t...

Variation in stream diatom communities in relation to water quality and catchment variables in a boreal, urbanized region.

PubMed

Teittinen, Anette; Taka, Maija; Ruth, Olli; Soininen, Janne

2015-10-15

Intensive anthropogenic land use such as urbanization alters the hydrological cycle, water chemistry and physical habitat characteristics, thus impairing stream physicochemical and biological quality. Diatoms are widely used to assess stream water quality as they integrate water chemistry temporally and reflect the joint influence of multiple stressors on stream biota. However, knowledge of the major community patterns of diatoms in urban streams remains limited especially in boreal regions. The aim of this study was to examine the effects of water chemistry and catchment characteristics on stream diatom communities, and to test the performance of the Index of Pollution Sensitivity (IPS) as a stream water quality indicator across an urban-to-rural gradient in southern Finland. Diatom community structure and species richness were related to local-scale variables such as water temperature, aluminium concentration, and electrical conductivity, which were in turn influenced by patterns in catchment land use and land cover. Diatoms reflected the intensity of human activities as more intensive land use increased the occurrence of pollution-tolerant species. The change in community structure along the land use intensity gradient was accompanied by a distinct decline in species richness. On the contrary, the IPS index failed to indicate differences in water quality along the urban-to-rural gradient as no consistent differences in the IPS values were found. Our results highlight the joint influence of multifaceted factors that underlie diatom patterns, and show that diatom biodiversity can be used as cost-effective metric indicating urban stream conditions. However, the IPS index turned out to be an unsuitable tool for assessing water quality among these streams. Copyright © 2015 Elsevier B.V. All rights reserved.

Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms.

PubMed

Young, Jodi N; Heureux, Ana M C; Sharwood, Robert E; Rickaby, Rosalind E M; Morel, François M M; Whitney, Spencer M

2016-05-01

While marine phytoplankton rival plants in their contribution to global primary productivity, our understanding of their photosynthesis remains rudimentary. In particular, the kinetic diversity of the CO2-fixing enzyme, Rubisco, in phytoplankton remains unknown. Here we quantify the maximum rates of carboxylation (k cat (c)), oxygenation (k cat (o)), Michaelis constants (K m) for CO2 (K C) and O2 (K O), and specificity for CO2 over O2 (SC/O) for Form I Rubisco from 11 diatom species. Diatom Rubisco shows greater variation in K C (23-68 µM), SC/O (57-116mol mol(-1)), and K O (413-2032 µM) relative to plant and algal Rubisco. The broad range of K C values mostly exceed those of C4 plant Rubisco, suggesting that the strength of the carbon-concentrating mechanism (CCM) in diatoms is more diverse, and more effective than previously predicted. The measured k cat (c) for each diatom Rubisco showed less variation (2.1-3.7s(-1)), thus averting the canonical trade-off typically observed between K C and k cat (c) for plant Form I Rubisco. Uniquely, a negative relationship between K C and cellular Rubisco content was found, suggesting variation among diatom species in how they allocate their limited cellular resources between Rubisco synthesis and their CCM. The activation status of Rubisco in each diatom was low, indicating a requirement for Rubisco activase. This work highlights the need to better understand the correlative natural diversity between the Rubisco kinetics and CCM of diatoms and the underpinning mechanistic differences in catalytic chemistry among the Form I Rubisco superfamily. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Large variation in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms

PubMed Central

Young, Jodi N.; Heureux, Ana M.C.; Sharwood, Robert E.; Rickaby, Rosalind E.M.; Morel, François M.M.; Whitney, Spencer M.

2016-01-01

While marine phytoplankton rival plants in their contribution to global primary productivity, our understanding of their photosynthesis remains rudimentary. In particular, the kinetic diversity of the CO2-fixing enzyme, Rubisco, in phytoplankton remains unknown. Here we quantify the maximum rates of carboxylation (k cat c), oxygenation (k cat o), Michaelis constants (K m) for CO2 (K C) and O2 (K O), and specificity for CO2 over O2 (SC/O) for Form I Rubisco from 11 diatom species. Diatom Rubisco shows greater variation in K C (23–68 µM), SC/O (57–116mol mol−1), and K O (413–2032 µM) relative to plant and algal Rubisco. The broad range of K C values mostly exceed those of C4 plant Rubisco, suggesting that the strength of the carbon-concentrating mechanism (CCM) in diatoms is more diverse, and more effective than previously predicted. The measured k cat c for each diatom Rubisco showed less variation (2.1–3.7s−1), thus averting the canonical trade-off typically observed between K C and k cat c for plant Form I Rubisco. Uniquely, a negative relationship between K C and cellular Rubisco content was found, suggesting variation among diatom species in how they allocate their limited cellular resources between Rubisco synthesis and their CCM. The activation status of Rubisco in each diatom was low, indicating a requirement for Rubisco activase. This work highlights the need to better understand the correlative natural diversity between the Rubisco kinetics and CCM of diatoms and the underpinning mechanistic differences in catalytic chemistry among the Form I Rubisco superfamily. PMID:27129950

Static vs dynamic settlement and adhesion of diatoms to ship hull coatings.

PubMed

Zargiel, Kelli A; Swain, Geoffrey W

2014-01-01

Many experiments utilize static immersion tests to evaluate the performance of ship hull coatings. These provide valuable data; however, they do not accurately represent the conditions both the hull and fouling organisms encounter while a ship is underway. This study investigated the effect of static and dynamic immersion on the adhesion and settlement of diatoms to one antifouling coating (BRA 640), four fouling-release coatings (Intersleek(®) 700, Intersleek(®) 900, Hempasil X3, and Dow Corning 3140) and one standard surface (Intergard(®) 240 Epoxy). Differences in community composition were observed between the static and dynamic treatments. Achnanthes longipes was present on all coatings under static immersion, but was not present under dynamic immersion. This was also found for diatoms in the genera Bacillaria and Gyrosigma. Melosira moniformis was the only diatom present under dynamic conditions, but not static conditions. Several common fouling diatom genera were present on panels regardless of treatment: Amphora, Cocconeis, Entomoneis Cylindrotheca, Licmophora, Navicula, Nitzschia, Plagiotropis, and Synedra. Biofilm adhesion, diatom abundance and diatom diversity were found to be significantly different between static and dynamic treatments; however, the difference was dependent on coating and sampling date. Several coatings (Epoxy, DC 3140 and IS 700) had significantly higher biofilm adhesion on dynamically treated panels on at least one of the four sampling dates, while all coatings had significantly higher diatom abundance on at least one sampling date. Diversity was significantly greater on static panels than dynamic panels for Epoxy, IS 700 and HX3 at least once during the sampling period. The results demonstrate how hydrodynamic stress will significantly influence the microfouling community. Dynamic immersion testing is required to fully understand how antifouling surfaces will respond to biofilm formation when subjected to the stresses experienced by a ship underway.

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta).

PubMed

Parks, Matthew B; Nakov, Teofil; Ruck, Elizabeth C; Wickett, Norman J; Alverson, Andrew J

2018-03-01

Diatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole-genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well. We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species. Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks-based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades. Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.

Summer Epiphytic Diatoms from Terra Nova Bay and Cape Evans (Ross Sea, Antarctica) - A Synthesis and Final Conclusions

PubMed Central

Majewska, Roksana; Convey, Peter; De Stefano, Mario

2016-01-01

Despite recent advances in polar marine biology and related fields, many aspects of the ecological interactions that are crucial for the functioning of Antarctic shallow water habitats remain poorly understood. Although epiphytic diatoms play an essential role in the Antarctic marine food web, basic information regarding their ecology, biodiversity and biogeography is largely unavailable. Here, we synthesise studies on Ross Sea epiphytic diatoms collected during 11 summer Antarctic expeditions between the years 1989/90 and 2011/12, presenting a full list of diatom taxa associated with three macroalgal species (Iridaea cordata, Phyllophora antarctica, and Plocamium cartilagineum) and their epiphytic sessile fauna. Diatom communities found during the three summer months at various depths and sampling stations differed significantly in terms of species composition, growth form structure and abundances. Densities ranged from 21 to >8000 cells mm-2, and were significantly higher on the surface of epiphytic micro-fauna than on any of the macroalgal species examined. Generally, host organisms characterized by higher morphological heterogeneity (sessile microfauna, ramified Plocamium) supported richer diatom communities than those with more uniform surfaces (Iridaea). Differences between epiphytic communities associated with different macroalgae were reflected better in species composition than in growth form structure. The latter changed significantly with season, which was related strongly to the changing ice conditions. A general trend towards an increasing number of erect forms in deeper waters and tube-dwelling diatoms in the shallowest sites (2–5 m) was also observed. This study explores further important and largely previously unknown aspects of relationships and interactions between Antarctic epiphytic diatoms and their micro- and macro-environments. PMID:27078637

Variations in diatom communities at genus and species levels in peatlands (central China) linked to microhabitats and environmental factors.

PubMed

Chen, Xu; Bu, Zhaojun; Stevenson, Mark A; Cao, Yanmin; Zeng, Linghan; Qin, Bo

2016-10-15

Peatlands are a specialized type of organic wetlands, fulfilling essential roles as global carbon sinks, headwaters of rivers and biodiversity hotspots. Despite their importance, peatlands are being lost at an alarming rate due to human disturbance and climatic variability. Both the scientific and regulatory communities have focused considerable attention on developing tools for assessing environmental changes in peatlands. Diatoms are widely used in biomonitoring studies of lakes, rivers and streams as they have high abundance, specific ecological preferences and can respond rapidly to environmental change. However, diatom-based assessment studies in peatlands remain limited. The aims of this study were to identify indicator species and genus for three types of habitats (hummocks, hollows and ditch edges) in peatlands (central China), to examine the effects of physiochemical factors on diatom composition at genus and species levels, and to compare the efficiency of species- and genus-level identification in environmental assessment. Our results revealed that hummocks were characterized by drought-tolerant diatoms, while hollows were dominated by species and genus preferring wet conditions. Ditch edges were characterized by diatoms with different life strategies. Depth to water table, redox potential, conductivity and calcium were significant predictors of both genus- and species-level composition. According to ordination analyses, pH was not correlated with species composition while it was a significant factor associated with genus-level composition. Genus-level composition outperformed species composition in describing the response of diatoms to environmental variables. Our results indicate that diatoms can be useful environmental indicators of peatlands, and show that genus-level taxonomic analysis can be a potential tool for assessing environmental change in peatlands. Copyright © 2016 Elsevier B.V. All rights reserved.

Thick-shelled, grazer-protected diatoms decouple ocean carbon and silicon cycles in the iron-limited Antarctic Circumpolar Current

PubMed Central

Assmy, Philipp; Smetacek, Victor; Montresor, Marina; Klaas, Christine; Henjes, Joachim; Strass, Volker H.; Arrieta, Jesús M.; Bathmann, Ulrich; Berg, Gry M.; Breitbarth, Eike; Cisewski, Boris; Friedrichs, Lars; Fuchs, Nike; Herndl, Gerhard J.; Jansen, Sandra; Krägefsky, Sören; Latasa, Mikel; Peeken, Ilka; Röttgers, Rüdiger; Scharek, Renate; Schüller, Susanne E.; Steigenberger, Sebastian; Webb, Adrian; Wolf-Gladrow, Dieter

2013-01-01

Diatoms of the iron-replete continental margins and North Atlantic are key exporters of organic carbon. In contrast, diatoms of the iron-limited Antarctic Circumpolar Current sequester silicon, but comparatively little carbon, in the underlying deep ocean and sediments. Because the Southern Ocean is the major hub of oceanic nutrient distribution, selective silicon sequestration there limits diatom blooms elsewhere and consequently the biotic carbon sequestration potential of the entire ocean. We investigated this paradox in an in situ iron fertilization experiment by comparing accumulation and sinking of diatom populations inside and outside the iron-fertilized patch over 5 wk. A bloom comprising various thin- and thick-shelled diatom species developed inside the patch despite the presence of large grazer populations. After the third week, most of the thinner-shelled diatom species underwent mass mortality, formed large, mucous aggregates, and sank out en masse (carbon sinkers). In contrast, thicker-shelled species, in particular Fragilariopsis kerguelensis, persisted in the surface layers, sank mainly empty shells continuously, and reduced silicate concentrations to similar levels both inside and outside the patch (silica sinkers). These patterns imply that thick-shelled, hence grazer-protected, diatom species evolved in response to heavy copepod grazing pressure in the presence of an abundant silicate supply. The ecology of these silica-sinking species decouples silicon and carbon cycles in the iron-limited Southern Ocean, whereas carbon-sinking species, when stimulated by iron fertilization, export more carbon per silicon. Our results suggest that large-scale iron fertilization of the silicate-rich Southern Ocean will not change silicon sequestration but will add carbon to the sinking silica flux. PMID:24248337

Molecular tools for the selective detection of nine diatom species biomarkers of various water quality levels.

PubMed

Cimarelli, Lucia; Singh, Kumar Saurabh; Mai, Nguyen Thi Nhu; Dhar, Bidhan Chandra; Brandi, Anna; Brandi, Letizia; Spurio, Roberto

2015-05-22

Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

Trace metals, PCBs, and PAHs in benthic (epipelic) diatoms from intertidal sediments; a pilot study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stronkhorst, J.; Misdorp, R.; Vos, P.C.

1994-06-01

Intertidal sediments in many estuaries around the world have a history of contamination resulting from long term discharges of industrial, agricultural and domestic waste effluents. These contaminated sediments are now regarded as a major source of toxicants for bottom-related organisms which, in turn, may pass on certain contaminants (e.g. methylmercury, polychlorinated biphenyls (PCBs)) to organisms higher in the foodchain. Many studies have been conducted on the contamination of benthic macrofauna, estuarine fish and birds, but to our knowledge no research has yet been carried out on benthic diatoms which form the lowest trophic level of an intertidal ecosystem. Research onmore » the effects of micro-contaminants on primary producers in marine ecosystems is mainly performed with phytoplankton. In the estuaries of temperate regions, benthic diatoms make a significant contribution to primary production in the ecosystem and are predated especially by deposit feeding Polychaete and Mollusca. Knowledge of the level of contamination in benthic diatoms is of major importance to recognize possible effects on growth rate and species composition of the benthic diatom populations and to understand the accumulation of toxicants into the foodchain. For chemical analysis it is difficult to obtain [open quote]pure[close quote] samples of benthic diatoms because they form part of the sediment. A similar problem occurs with the sampling of phytoplankton in turbid estuarine waters. The aim of this pilot study was (a) to improve a trap technique to collect pure samples of benthic diatoms of at least 2 gram dry weight for analysis of trace metals, PCBs and polyaromatic hydrocarbons (PAHs) and (b) to compare the concentrations in benthic diatoms with levels in sediment and some bottom-related organisms. 16 refs., 2 figs., 2 tabs.« less

Scale-dependent effects of land cover on water physico-chemistry and diatom-based metrics in a major river system, the Adour-Garonne basin (South Western France).

PubMed

Tudesque, Loïc; Tisseuil, Clément; Lek, Sovan

2014-01-01

The scale dependence of ecological phenomena remains a central issue in ecology. Particularly in aquatic ecology, the consideration of the accurate spatial scale in assessing the effects of landscape factors on stream condition is critical. In this context, our study aimed at assessing the relationships between multi-spatial scale land cover patterns and a variety of water quality and diatom metrics measured at the stream reach level. This investigation was conducted in a major European river system, the Adour-Garonne river basin, characterized by a wide range of ecological conditions. Redundancy analysis (RDA) and variance partitioning techniques were used to disentangle the different relationships between land cover, water-chemistry and diatom metrics. Our results revealed a top-down "cascade effect" indirectly linking diatom metrics to land cover patterns through water physico-chemistry, which occurred at the largest spatial scales. In general, the strength of the relationships between land cover, physico-chemistry, and diatoms was shown to increase with the spatial scale, from the local to the basin scale, emphasizing the importance of continuous processes of accumulation throughout the river gradient. Unexpectedly, we established that the influence of land cover on the diatom metric was of primary importance both at the basin and local scale, as a result of discontinuous but not necessarily antagonist processes. The most detailed spatial grain of the Corine land cover classification appeared as the most relevant spatial grain to relate land cover to water chemistry and diatoms. Our findings provide suitable information to improve the implementation of effective diatom-based monitoring programs, especially within the scope of the European Water Framework Directive. © 2013 Elsevier B.V. All rights reserved.

Distinctive Photosystem II Photoinactivation and Protein Dynamics in Marine Diatoms1[W

PubMed Central

Wu, Hongyan; Cockshutt, Amanda M.; McCarthy, Avery; Campbell, Douglas A.

2011-01-01

Diatoms host chlorophyll a/c chloroplasts distinct from green chloroplasts. Diatoms now dominate the eukaryotic oceanic phytoplankton, in part through their exploitation of environments with variable light. We grew marine diatoms across a range of temperatures and then analyzed their PSII function and subunit turnover during an increase in light to mimic an upward mixing event. The small diatom Thalassiosira pseudonana initially responds to increased photoinactivation under blue or white light with rapid acceleration of the photosystem II (PSII) repair cycle. Increased red light provoked only modest PSII photoinactivation but triggered a rapid clearance of a subpool of PsbA. Furthermore, PsbD and PsbB content was greater than PsbA content, indicating a large pool of partly assembled PSII repair cycle intermediates lacking PsbA. The initial replacement rates for PsbD (D2) were, surprisingly, comparable to or higher than those for PsbA (D1), and even the supposedly stable PsbB (CP47) dropped rapidly upon the light shift, showing a novel aspect of rapid protein subunit turnover in the PSII repair cycle in small diatoms. Under sustained high light, T. pseudonana induces sustained nonphotochemical quenching, which correlates with stabilization of PSII function and the PsbA pool. The larger diatom Coscinodiscus radiatus showed generally similar responses but had a smaller allocation of PSII complexes relative to total protein content, with nearly equal stiochiometries of PsbA and PsbD subunits. Fast turnover of multiple PSII subunits, pools of PSII repair cycle intermediates, and photoprotective induction of nonphotochemical quenching are important interacting factors, particularly for small diatoms, to withstand and exploit high, fluctuating light. PMID:21617029

Lipophilic pigments from cyanobacterial (blue-green algal) and diatom mats in Hamelin Pool, Shark Bay, Western Australia

NASA Technical Reports Server (NTRS)

Palmisano, A. C.; Summons, R. E.; Cronin, S. E.; Des Marais, D. J.

1989-01-01

Lipophilic pigments were examined in microbial mat communities dominated by cyanobacteria in the intertidal zone and by diatoms in the subtidal and sublittoral zones of Hamelin Pool, Shark Bay, Western Australia. These microbial mats have evolutionary significance because of their similarity to lithfied stromatolites from the Proterozoic and Early Paleozoic eras. Fucoxanthin, diatoxanthin, diadinoxanthin, beta-carotene, and chlorophylls a and c characterized the diatom mats, whereas cyanobacterial mats contained myxoxanthophyll, zeaxanthin, echinenone, beta-carotene, chlorophyll a and, in some cases, sheath pigment. The presence of bacteriochlorophyll a within the mats suggest a close association of photosynthetic bacteria with diatoms and cyanobacteria. The high carotenoids : chlorophyll a ratios (0.84-2.44 wt/wt) in the diatom mats suggest that carotenoids served a photoprotective function in this high light environment. By contrast, cyanobacterial sheath pigment may have largely supplanted the photoprotective role of carotenoids in the intertidal mats.

X-ray fluorescence mapping of mercury on suspended mineral particles and diatoms in a contaminated freshwater system

NASA Astrophysics Data System (ADS)

Gu, B.; Mishra, B.; Miller, C.; Wang, W.; Lai, B.; Brooks, S. C.; Kemner, K. M.; Liang, L.

2014-05-01

Mercury (Hg) bioavailability and geochemical cycling is affected by its partitioning between the aqueous and particulate phases. We applied X-ray fluorescence (XRF) microprobes to directly visualize and quantify the spatial localization of Hg and its correlations with other elements of interest on suspended particles from a Hg contaminated freshwater system. Up to 175 μg g-1 Hg is found on suspended particles. Mercury is heterogeneously distributed among phytoplankton (e.g., diatoms) and mineral particles that are rich in iron oxides and natural organic matter (NOM), possibly as Hg-NOM-iron oxide ternary complexes. The diatom-bound Hg is mostly found on outer surfaces of the cells, suggesting passive sorption of inorganic Hg on diatoms. Our results indicate that localized sorption of Hg onto suspended particles, including diatoms and NOM-coated oxide minerals, is an important sink for Hg in natural aquatic environments.

Relationships between diatoms and tidal environments in Oregon and Washington, USA

USGS Publications Warehouse

Sawai, Yuki; Horton, Benjamin P.; Kemp, Andrew C.; Hawkes, Andrea D.; Nagumo, Tamostsu; Nelson, Alan R.

2016-01-01

A new regional dataset comprising 425 intertidal diatom taxa from 175 samples from 11 ecologically diverse Oregon and Washington estuaries illustrates the importance of compiling a large modern dataset from a range of sites. Cluster analyses and detrended correspondence analysis of the diatom assemblages identify distinct vertical zones within supratidal, intertidal and subtidal environments at six of the 11 study sites, but the abundance of some of the most common species varies widely among and within sites. Canonical correspondence analysis of the regional dataset shows relationships between diatom species and tidal exposure, salinity and substratum (grain size and organic content). Correspondence analyses of local datasets show higher values of explained variation than the analysis of the combined regional dataset. Our results emphasize that studies of the autecology of diatom species require many samples from a range of modern environments to adequately characterize species–environment relationships.

Windblown Pliocene diatoms and East Antarctic Ice Sheet retreat

PubMed Central

Scherer, Reed P.; DeConto, Robert M.; Pollard, David; Alley, Richard B.

2016-01-01

Marine diatoms in tillites along the Transantarctic Mountains (TAMs) have been used to suggest a diminished East Antarctic Ice Sheet (EAIS) during Pliocene warm periods. Updated ice-sheet modelling shows significant Pliocene EAIS retreat, creating marine embayments into the Wilkes and Aurora basins that were conducive to high diatom productivity and rapid accumulation of diatomaceous sediments. Here we show that subsequent isostatic uplift exposed accumulated unconsolidated marine deposits to wind erosion. We report new atmospheric modelling utilizing Pliocene climate and derived Antarctic landscapes indicating that prevailing mid-altitude winds transported diatoms towards the TAMs, dominantly from extensive emerged coastal deposits of the Aurora Basin. This result unifies leading ideas from competing sides of a contentious debate about the origin of the diatoms in the TAMs and their link to EAIS history, supporting the view that parts of the EAIS are vulnerable to relatively modest warming, with possible implications for future sea-level rise. PMID:27649516

Radioisotopic Method for Measuring Cell Division Rates of Individual Species of Diatoms from Natural Populations †

PubMed Central

Rivkin, Richard B.

1986-01-01

Silicon is an essential element for diatom frustule synthesis and is usually taken up only by dividing cells. With 68Ge, a radioactive analog of Si, the cell cycle marker event of frustule formation was identified for individual species of diatom. The frequency of cells within a population undergoing this division event was estimated, and the cell division rate was calculated. In laboratory cultures, these rates of cell division and those calculated from changes in cell numbers were similar. By dual labeling with 68Ge(OH)4 and NaH14CO3, rates of cell division and photosynthesis were coincidently measured for diatoms both in laboratory cultures and when isolated from natural populations in estuarine, offshore, and polar environments. These techniques permit the coupling between photosynthesis and cell division to be examined in situ for individual species of diatom. PMID:16347039

On continuous and discontinuous approaches for modeling groundwater flow in heterogeneous media using the Numerical Manifold Method: Model development and comparison

NASA Astrophysics Data System (ADS)

Hu, Mengsu; Wang, Yuan; Rutqvist, Jonny

2015-06-01

One major challenge in modeling groundwater flow within heterogeneous geological media is that of modeling arbitrarily oriented or intersected boundaries and inner material interfaces. The Numerical Manifold Method (NMM) has recently emerged as a promising method for such modeling, in its ability to handle boundaries, its flexibility in constructing physical cover functions (continuous or with gradient jump), its meshing efficiency with a fixed mathematical mesh (covers), its convenience for enhancing approximation precision, and its integration precision, achieved by simplex integration. In this paper, we report on developing and comparing two new approaches for boundary constraints using the NMM, namely a continuous approach with jump functions and a discontinuous approach with Lagrange multipliers. In the discontinuous Lagrange multiplier method (LMM), the material interfaces are regarded as discontinuities which divide mathematical covers into different physical covers. We define and derive stringent forms of Lagrange multipliers to link the divided physical covers, thus satisfying the continuity requirement of the refraction law. In the continuous Jump Function Method (JFM), the material interfaces are regarded as inner interfaces contained within physical covers. We briefly define jump terms to represent the discontinuity of the head gradient across an interface to satisfy the refraction law. We then make a theoretical comparison between the two approaches in terms of global degrees of freedom, treatment of multiple material interfaces, treatment of small area, treatment of moving interfaces, the feasibility of coupling with mechanical analysis and applicability to other numerical methods. The newly derived boundary-constraint approaches are coded into a NMM model for groundwater flow analysis, and tested for precision and efficiency on different simulation examples. We first test the LMM for a Dirichlet boundary and then test both LMM and JFM for an idealized heterogeneous model, comparing the numerical results with analytical solutions. Then we test both approaches for a heterogeneous model and compare the results of hydraulic head and specific discharge. We show that both approaches are suitable for modeling material boundaries, considering high accuracy for the boundary constraints, the capability to deal with arbitrarily oriented or complexly intersected boundaries, and their efficiency using a fixed mathematical mesh.

Molecular three-body Brauner-Briggs-Klar theory for ion-impact ionization of molecules

NASA Astrophysics Data System (ADS)

Ghanbari-Adivi, E.

2016-12-01

Molecular three-body Brauner-Briggs-Klar (M3BBK) theory is developed to study the single ionization of diatomic molecules by ion impact. The orientation-averaged molecular orbital (OAMO) approximation is used to reduce the required computer time without sacrificing the performance of the method. The post-collision interaction (PCI) between the scattered projectile and the ejected electron is included. The theory is applied to collision of protons with hydrogen molecules. Results are obtained for two different kinematical regimes: i) fast collisions and low emission energies, and ii) not so fast collisions and higher emission energies. For both considered regimes, experimental fully differential cross-sections as well as different theoretical calculations are available for comparison. These comparisons are carried out and discussed.

Near-field excitation exchange between motionless point atoms located near the conductive surface

NASA Astrophysics Data System (ADS)

Kuraptsev, Aleksei S.; Sokolov, Igor M.

2018-04-01

On the basis of quantum microscopic approach we study the excitation dynamics of two motionless point atoms located near the perfectly conducting mirror. We have analyzed the spontaneous decay rate of individual atoms near the mirror as well as the strength of dipole-dipole interaction between different atoms. It is shown that the spontaneous decay rate of an excited atom significantly depends on the distance from this atom to the mirror. In the case when the interatomic separation is less or comparable with the wavelength of resonant radiation, the spontaneous decay dynamics of an excited atom is described by multi-exponential law. It depends both the interatomic separation and the spatial orientation of diatomic quasimolecule.

Diatoms on Earth, Comets, Europa and in Interstellar Space

NASA Astrophysics Data System (ADS)

Hoover, Richard B.; Hoyle, Fred; Wickramasinghe, N. C.; Hoover, Miriam J.; Al-Mufti, S.

There exists a close correspondence between the measured infrared properties of diatoms and the infrared spectrum of interstellar dust as observed in the Trapezium nebula and toward the galactic center source GC-IRS 7. Diatoms and bacteria also exhibit an absorbance peak near 2200 Å, which is found to agree with the observed ultraviolet absorbance properties of interstellar grains. We review the observational data and consider the known properties of diatoms and bacteria. It is suggested that these characteristics are consistent with the concept of a cosmic microbiological system in which these or similar microorganisms might exist on comets, Europa and in interstellar space.

3D Tracking of Diatom Motion in Turbulent Flow

NASA Astrophysics Data System (ADS)

Variano, E. A.; Brandt, L.; Sardina, G.; Ardekani, M.; Pujara, N.; Ayers, S.; Du Clos, K.; Karp-Boss, L.; Jumars, P. A.

2016-02-01

We present laboratory measurements of single-celled and chain forming diatom motion in a stirred turbulence tank. The overarching goal is to explore whether diatoms track flow with fidelity (passive tracers) or whether interactions with cell density and shape result in biased trajectories that alter settling velocities. Diatom trajectories are recorded in 3D using a stereoscopic, calibrated tracking tool. Turbulence is created in a novel stirred tank, designed to create motions that match those found in the ocean surface mixed layer at scales less than 10 cm. The data are analyzed for evidence of enhanced particle clustering, an indicator of turbulently altered settling rates

A land-use and water-quality history of White Rock Lake Reservoir, Dallas, Texas, based on paleolimnological analyses

USGS Publications Warehouse

Platt, Bradbury J.; Van Metre, P.C.

1997-01-01

White Rock Lake reservoir in Dallas, Texas contains a 150-cm sediment record of silty clay that documents land-use changes since its construction in 1912. Pollen analysis corroborates historical evidence that between 1912 and 1950 the watershed was primarily agricultural. Land disturbance by plowing coupled with strong and variable spring precipitation caused large amounts of sediment to enter the lake during this period. Diatoms were not preserved at this time probably because of low productivity compared to diatom dissolution by warm, alkaline water prior to burial in the sediments. After 1956, the watershed became progressively urbanized. Erosion decreased, land stabilized, and pollen of riparian trees increased as the lake water became somewhat less turbid. By 1986 the sediment record indicates that diatom productivity had increased beyond rates of diatom destruction. Neither increased nutrients nor reduced pesticides can account for increased diatom productivity, but grain size studies imply that before 1986 diatoms were light limited by high levels of turbidity. This study documents how reservoirs may relate to land-use practices and how watershed management could extend reservoir life and improve water quality.

Chitinase producing bacteria with direct algicidal activity on marine diatoms

PubMed Central

Li, Yi; Lei, Xueqian; Zhu, Hong; Zhang, Huajun; Guan, Chengwei; Chen, Zhangran; Zheng, Wei; Fu, Lijun; Zheng, Tianling

2016-01-01

Chitinase producing bacteria can involve extensively in nutrient cycling and energy flow in the aquatic environment through degradation and utilization of chitin. It is well known that diatoms cells are encased by box-like frustules composed of chitin. Thus the chitin containing of diatoms shall be a natural target of chitinase producing bacteria, however, the interaction between these two organismic groups has not been studied thus far. Therefore, in this study, the algicidal mechanism of one chitinase producing bacterium (strain LY03) on Thalassiosira pseudonana was investigated. The algicidal range and algicidal mode of strain LY03 were first studied, and then bacterial viability, chemotactic ability and direct interaction characteristic between bacteria and diatom were also confirmed. Finally, the characteristic of the intracellular algicidal substance was identified and the algicidal mechanism was determined whereby algicidal bacterial cells showed chemotaxis to algal cells, fastened themselves on algal cells with their flagella, and then produced chitinase to degrade algal cell walls, and eventually caused algal lysis and death. It is the first time to investigate the interaction between chitinase producing bacteria and diatoms, and this novel special interaction mode was confirmed in this study, which will be helpful in protection and utilization of diatoms resources. PMID:26902175

Chitinase producing bacteria with direct algicidal activity on marine diatoms.

PubMed

Li, Yi; Lei, Xueqian; Zhu, Hong; Zhang, Huajun; Guan, Chengwei; Chen, Zhangran; Zheng, Wei; Fu, Lijun; Zheng, Tianling

2016-02-23

Chitinase producing bacteria can involve extensively in nutrient cycling and energy flow in the aquatic environment through degradation and utilization of chitin. It is well known that diatoms cells are encased by box-like frustules composed of chitin. Thus the chitin containing of diatoms shall be a natural target of chitinase producing bacteria, however, the interaction between these two organismic groups has not been studied thus far. Therefore, in this study, the algicidal mechanism of one chitinase producing bacterium (strain LY03) on Thalassiosira pseudonana was investigated. The algicidal range and algicidal mode of strain LY03 were first studied, and then bacterial viability, chemotactic ability and direct interaction characteristic between bacteria and diatom were also confirmed. Finally, the characteristic of the intracellular algicidal substance was identified and the algicidal mechanism was determined whereby algicidal bacterial cells showed chemotaxis to algal cells, fastened themselves on algal cells with their flagella, and then produced chitinase to degrade algal cell walls, and eventually caused algal lysis and death. It is the first time to investigate the interaction between chitinase producing bacteria and diatoms, and this novel special interaction mode was confirmed in this study, which will be helpful in protection and utilization of diatoms resources.

Diversity dynamics of marine planktonic diatoms across the Cenozoic.

PubMed

Rabosky, Daniel L; Sorhannus, Ulf

2009-01-08

Diatoms are the dominant group of phytoplankton in the modern ocean. They account for approximately 40% of oceanic primary productivity and over 50% of organic carbon burial in marine sediments. Owing to their role as a biological carbon pump and effects on atmospheric CO(2) levels, there is great interest in elucidating factors that influenced the rapid rise in diatom diversity during the past 40 million years. Two biotic controls on diversification have been proposed to explain this diversity increase: (1) geochemical coupling between terrestrial grasslands and marine ecosystems through the global silicon cycle; and (2) competitive displacement of other phytoplankton lineages. However, these hypotheses have not been tested using sampling-standardized fossil data. Here we show that reconstructions of species diversity in marine phytoplankton reject these proposed controls and suggest a new pattern for oceanic diatom diversity across the Cenozoic. Peak species diversity in marine planktonic diatoms occurred at the Eocene-Oligocene boundary and was followed by a pronounced decline, from which diversity has not recovered. Although the roles of abiotic and biotic drivers of diversification remain unclear, major features of oceanic diatom evolution are decoupled from both grassland expansion and competition among phytoplankton groups.

Diatom communities on commercial biocidal fouling control coatings after one year of immersion in the marine environment.

PubMed

Muthukrishnan, Thirumahal; Dobretsov, Sergey; De Stefano, Mario; Abed, Raeid M M; Kidd, Barry; Finnie, Alistair A

2017-08-01

Little is known about the effect of commercial biocidal fouling control coatings on fouling diatom communities and their growth forms after long periods of exposure in the marine tropical environment. The current study investigated the abundance and composition of fouling diatom communities developed on 11 commercially available biocidal antifouling coatings, covering the three main technology types in recent historic use (Self-Polishing Copolymers, Self-Polishing Hybrid and Controlled Depletion Polymers) after one year of static immersion at two locations in Muscat, Oman (Marina Shangri La and Marina Bandar Rowdha). Light microscopy demonstrated that the total abundance of diatoms and the relative abundance of growth forms were significantly affected by the choice of biocidal antifouling coating and experimental location. Using scanning electron microscopy, a total of 21 diatom genera were identified which were grouped into adnate, motile, plocon and erect growth forms. The adnate growth forms, mainly the genera Amphora, Cocconeis and Mastogloia, dominated the other growth forms in terms of their relative abundance. Current results revealed the importance of exposure location and choice of biocidal antifouling coating on the relative abundance of diatom growth forms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Relation of phytoplankton species to ecosystem definition in the northwest Atlantic using remote sensing data

NASA Astrophysics Data System (ADS)

Devred, Emmanuel; Sathyendranath, Shubha; Fuentes-yaco, Cesar; Maass, Heidi; Platt, Trevor

2005-08-01

In this work, we present a new method for dynamic assignment of the boundaries of the ecological provinces of the North West Atlantic. The results are compared with the distribution of diatoms in the study area. Both analyses rely on ocean-colour data for the region. Diatoms were identified using remoteely-sensed data on the basis of their species-dependent absorption characteristics, which were embedded in a simple reflectance model(Sathyendranath et al., 2004). Maps of diatom distributions were produced for the area. Satellite-derived chlorophyll biomass and sea surface temperature (MODIS data) for the same period were used to redefine, in a dynamic way, the static borders of the ecological provinces (Sathyendranath et al., 1995; Longhurst 1998). The analyses were carried on two-week composite images, at different times of the year (April-May, July and October), to examine seasonal variability in the boundaries. The boundaries of provinces and the occurrence of diatoms were spatially coherent. Diatoms were favoured in rich waters on the continental shelf and in cold waters at high latitudes. In provinces labelled as oligotrophic (subtropical gyre and Gulf Stream), very negligible fractions of diatoms were found at any time of the year.

Differences between mono-generic and mixed diatom silicon isotope compositions trace present and past nutrient utilisation off Peru

NASA Astrophysics Data System (ADS)

Doering, Kristin; Ehlert, Claudia; Grasse, Patricia; Crosta, Xavier; Fleury, Sophie; Frank, Martin; Schneider, Ralph

2016-03-01

In this study we combine for the first time silicon (Si) isotope compositions of small mixed diatom species (δ30SibSiO2) and of large handpicked mono-generic (i.e. genus = Coscinodiscus) diatom samples (δ30SiCoscino) with diatom assemblages extracted from marine sediments in the Peruvian upwelling region in order to constrain present and past silicate utilisation. The extension of a previous core-top data set from the Peruvian shelf demonstrates that δ30SiCoscino values record near-complete Si utilisation, as these are similar to the isotopic composition of the subsurface source waters feeding the upwelling. In contrast, the δ30SibSiO2 of small mixed diatom species increase southward along the shelf as well as towards the shore. We attribute highest δ30SibSiO2 values partly to transient iron limitation but primarily to the gradual increase of Si isotope fractionation within the seasonal diatom succession, which are mainly recorded by small diatom species during intense bloom events. In contrast, lower δ30SibSiO2 values are related to initial Si isotope utilisation during periods of weak upwelling, when low Si(OH)4 concentrations do not permit intense blooms and small diatom species record substantially lower δ30Si signatures. As such, we propose that the intensity of the upwelling can be deduced from the offset between δ30SibSiO2 and δ30SiCoscino (Δ30Sicoscino-bSiO2), which is low for strong upwelling conditions and high for prevailing weak upwelling. We apply the information extracted from surface sediments to generate a record of the present-day main upwelling region covering the past 17,700 years and find that this location has also been characterized by a persistent offset (Δ30Sicoscino-bSiO2). By comparison with the diatom assemblages we show that the coastal upwelling system changed markedly between weak and strong upwelling conditions. In addition, our model calculations to quantify species-specific Si isotope fractionation effects based on the diatom assemblages indicate an overall minor influence that cannot explain the high amplitude in the measured δ30SibSiO2 record.

Diatoms (Class Bacillariophyceae) and geochemistry from annually laminated mid-Holocene sediments, west coast Canada: insights into abrupt climate change in the past

NASA Astrophysics Data System (ADS)

Chang, A.; Pedersen, T. F.

2009-04-01

A 115-year record of annually laminated sediments from Effingham Inlet, a small anoxic fjord on the west coast of Vancouver Island, British Columbia (49˚N, 125˚W), was analyzed for diatoms (species and abundances) and geochemistry (C and N isotopes, organic C and trace elements Ag, Cd, Re and Mo) from a piston core. The sediments were radiocarbon dated at approx. 4200-4400 years before present (yr BP) and show diatom enriched varves in the lower 70 years, with a sudden transition to diatom impoverished varves above. In the lower section, varves are thick (2-5 mm) and consist of well-defined Thalassiosira-Skeletonema-Chaetoceros spring bloom successions. Diatom concentrations average at 787 ± 733 million valves/g of dry sediment, del 15N at 7.0 ± 0.5 per mil, and organic C at 5.2 ± 0.5 wt. %. In the upper section, the varves are thinner (1-2 mm), do not clearly show the seasonal diatom succession, and contain increased terrigenous detritus. Diatom concentrations average at 388 ± 202 million valves/g with an increased relative abundance of benthic and freshwater taxa, del 15N at 7.3 ± 0.6 per mil and organic C at 5.7 ± 0.5 wt. %. Values of del 13C for both sections are similar, averaging at -24.0 ± 0.5 per mil. The trace element concentrations are quite variable throughout the section. However, several thin (<1 cm) nonlaminated intervals show decreased diatom abundances with concomitant increases in trace element concentrations, suggesting short-lived changes in surface productivity, upwelling and nutrient delivery, and/or anoxic conditions. The abrupt transition from diatom-rich to diatom-poor varves could reflect a shift in dominance of the North Pacific High and Aleutian Low atmospheric pressure systems over the northeast Pacific Ocean, not unlike the well-documented 1976/1977 climate regime shift which showed a change in upwelling and nutrient delivery. A transition between warm and sunny climates to cooler and wetter regimes at around 4000 yr BP has been noted in previous paleoenvironmental studies from British Columbia and the northern hemisphere in general. The Effingham Inlet sediment record data will also be compared with modern sediment trap data from the inlet.

Boron Isotopes in Diatoms: a Proxy for pH?

NASA Astrophysics Data System (ADS)

Donald, H.; Foster, G. L.; Poulton, A. J.; Moore, C. M.; Swann, G. E. A.; Hendry, K. R.

2016-12-01

High latitudes are important regions to consider in terms of ocean acidification, as they are climatically sensitive regions where the greenhouse gas CO2 is exchanged between the ocean and atmosphere. In theory, an improved understanding of these regions could be achieved using the boron isotope palaeo-pH proxy, in which CaCO3-based organisms including foraminifera are traditionally measured. The Southern Ocean is of particular interest in the global carbon cycle, however, foraminifera are scarce in sediments from this region. In contrast, siliceous diatoms are a dominant group of microfossils found within sediments, but as yet, the boron isotope-pH proxy has not been extended to opal. This is the major goal of the current study. Diatoms construct their frustules from biogenic silica by polymerising Si(OH)4, and boron content of these frustules, previously investigated by LA-ICP-MS (Mejía et al. 2013), is around 5-10 ppm. Here, current solution MC-ICP-MS methods used to measure boron isotopes in calcifying organisms have been adapted and developed for use with diatom opal. Preliminary results for sediment diatoms from the onset of major Northern Hemisphere glaciation will be presented (subarctic Northwest Pacific ODP site 882), as well as results for the cultured diatom species Thalassiosira weissflogii grown at varied pCO2. In light of these results, we will speculate on the nature of boron incorporation into diatom opal and its potential as an archive for palaeo-pH reconstructions.

The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean.

PubMed

Vincent, Flora J; Colin, Sébastien; Romac, Sarah; Scalco, Eleonora; Bittner, Lucie; Garcia, Yonara; Lopes, Rubens M; Dolan, John R; Zingone, Adriana; de Vargas, Colomban; Bowler, Chris

2018-04-01

Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterization of any such partnership is, however, limited, and an appraisal of the large-scale distribution and ecology of such consortia was never attempted. Here, observation of Tara Oceans samples from the Benguela Current led to the detection of an epibiotic association between a pennate diatom and a tintinnid ciliate. We identified the diatom as Fragilariopsis doliolus that possesses a unique feature to form barrel-shaped chains, associated with seven different genera of tintinnids including five previously undescribed associations. The organisms were commonly found together in the Atlantic and Pacific Ocean basins, and live observations of the interaction have been recorded for the first time. By combining confocal and scanning electron microscopy of individual consortia with the sequencing of high-resolution molecular markers, we analyzed their distribution in the global ocean, revealing morpho-genetically distinct tintinnid haplotypes and biogeographically structured diatom haplotypes. The diatom was among the most abundant in the global ocean. We show that the consortia were particularly prevalent in nutrient-replete conditions, rich in potential predators. These observations support the hypothesis of a mutualistic symbiosis, wherein diatoms acquire increased motility and tintinnids benefit from silicification through increased protection, and highlight that such associations may be more prevalent than currently appreciated.

The diatom flora of Lake Kinneret (Israel) - Paleolimnological evidence for Holocene climate change and human impact in the southeastern Mediterranean

NASA Astrophysics Data System (ADS)

Vossel, Hannah; Reed, Jane M.; Litt, Thomas

2015-04-01

The Mediterranean basin is a region of highly complex topography and climatic variability, such that our understanding of the past environmental variability is still limited. Diatoms (single-celled siliceous algae, Bacillariophyceae) are abundant, diverse and sensitive to a wide range of environmental parameters. They are often well preserved in lake sediment records, and have well-recognised potential to generate high-quality paleolimnological data. Diatoms remain one of the least-exploited proxies in Mediterranean palaeoclimate research. Here, we present results of diatom analysis of an 18 m sediment core from Lake Kinneret (Israel) as part of a multi-proxy study of Holocene climate change and human impact in the Levant (http://www.sfb806.uni-koeln.de). Results are compared with other proxy data including pollen, and with output data from regional climate modelling, to strengthen interpretation of environmental change in the southeastern Mediterranean. The results show remarkable shifts in the diatom flora over the last ca. 8,000 years. Preliminary investigations show that 98% of the diatom taxa can be classified as oligohalobous-indifferent and as alkaliphilous, as is typical of freshwater, alkaline lakes of open hydrology in limestone, karst-dominated catchments. Changes in the diatom data over time can be interpreted mainly in terms of productivity shifts, with a clear trend from oligotrophic at the base to hypereutrophic in the modern lake. The eutrophication trend accelerates after ca. 3,000 cal. yrs. BP, indicating the influence of increased human activity in the catchment, identified previously by analysis of the vegetational history (Schiebel, 2013). The analysis of the composition of the diatom flora also provides some evidence for lake-level fluctuations, as a proxy for shifts in moisture availability. Low lake-level stands are characterized by low diatom concentration and increased relative abundance of littoral taxa. High lake-level stands are marked by the clear dominance of planktonic species, such as Cyclotella ocellata PANTOCSEK and Cyclotella paleo-ocellata VOSSEL & VAN DE VIJVER (a newly described centric diatom which may be endemic (Vossel et al., 2015), in phases of high diatom concentration. Such inferred lake-level oscillations correlate well with the output from the climatic models from the Levant region, representing changes in moisture availability (Litt et al., 2012), although the signal is obscured in the last 3,000 years by the effects of anthropogenic eutrophication. References Litt, T.; Ohlwein, C.; Neumann, F. H.; Hense, A. & Stein, M. (2012): Holocene climate variability in the Levant from the Dead Sea pollen record. - Quat. Sci. Rev., 49: 95-105. Schiebel, V. (2013): Vegetation and climate history of the southern Levant during the last 30,000 years based on palynological investigation. - Unpublished PhD thesis. Vossel, H.; Reed, J. M.; Houk, V.; Cvetkoska, A. & Van de Vijver, B. (2015): Cyclotella paleo-ocellata, a new centric diatom (Bacillariophyta) from Lake Kinneret (Israel). Fottea, 15 (1), in press.

A Summary and Evaluation of Aquatic Environmental Data in Relation to Establishing Water Quality Criteria for Munitions-Unique Compounds. Part 3. White Phosphorus.

DTIC Science & Technology

1979-04-01

cellular disruption * from WP than the cyanophytes. Additionally, the principal storage products of diatoms are lipids (Duke and Reiman 1977). The...PA 555 pp. 60 Duke, E.L. and B.E.F. Reiman . 1977. The ultrastructure of the diatom cell. In: The biology of diatoms. 0. Werner, ed. Botanical

Genetic manipulation of competition for nitrate between heterotrophic bacteria and diatoms

DOE PAGES

Diner, Rachel E.; Schwenck, Sarah M.; McCrow, John P.; ...

2016-06-09

Diatoms are a dominant group of eukaryotic phytoplankton that contribute substantially to global primary production and the cycling of important elements such as carbon and nitrogen. Heterotrophic bacteria, including members of the gammaproteobacteria, are commonly associated with diatom populations and may rely on them for organic carbon while potentially competing with them for other essential nutrients. Considering that bacterioplankton drive oceanic release of CO 2 (i.e., bacterial respiration) while diatoms drive ocean carbon sequestration vial the biological pump, the outcome of such competition could influence the direction and magnitude of carbon flux in the upper ocean. Nitrate availability is commonlymore » a determining factor for the growth of diatom populations, particularly in coastal and upwelling regions. Diatoms as well as many bacterial species can utilize nitrate, however the ability of bacteria to compete for nitrate may be hindered by carbon limitation. Here we have developed a genetically tractable model system using the pennate diatom Phaeodactylurn tricomuturn and the widespread heterotrophic bacteria Alterornonas macleodii to examine carbon-nitrogen dynamics. While subsisting solely on P. tricomutum derived carbon. A. macleodii does not appear to be an effective competitor for nitrate, and may in fact benefit the diatom; particularly in stationary phase. However, allochthonous dissolved organic carbon addition in the form of pyruvate triggers A. macleodii proliferation and nitrate uptake, leading to reduced P. tricornutum growth. Nitrate reductase deficient mutants of A. macleodii ( ΔnasA) do not exhibit such explosive growth and associated competitive ability in response to allochthonous carbon when nitrate is the sole nitrogen source, but could survive by utilizing solely P. tricomutum-derived nitrogen. Furthermore, allocthonous carbon addition enables wild-type A. macleodii to rescue nitrate reductase deficient P. tricomutum populations from nitrogen starvation, and RNA-seq transcriptomic evidence supports nitrogen-based interactions between diatoms and bacteria at the molecular level. As a result, this study provides key insights into the roles of carbon and nitrogen in phytoplankton-bacteria dynamics and lays the foundation for developing a mechanistic understanding of these interactions using co-culturing and genetic manipulation.« less

Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta)

PubMed Central

2010-01-01

Background Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions. Results All isolates from the more regionally-localized population (population 2) possessed 1.94 ± 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1). The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history. Conclusions The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is consistent with a recent divergence between the populations, which are likely cryptic species. Genome size variation is known to occur in other diatom genera; we hypothesize that genome duplication may be an active and important mechanism of genetic and physiological diversification and speciation in diatoms. PMID:20044934

Distribution of Epiphytic Diatoms in a Sub-Tropical Estuary

NASA Astrophysics Data System (ADS)

Frankovich, T. A.; Gaiser, E. E.; Wachnicka, A.; Zieman, J. C.

2005-05-01

Within estuaries, seagrasses may represent an order of magnitude greater surface area relative to sediments for the colonization and growth of diatoms. Fossil diatom distributions have proven useful in inferring paleoenvironmental conditions. The strength of these inferences is dependent upon defining the environmental relationships of contempory diatom compositions. The present investigation characterized the modern epiphytic diatom flora on the seagrass Thalassia testudinum at seven sites in the sub-tropical Florida Bay estuary and at one Atlantic Ocean site east of the upper Florida Keys. These sites were sampled six times between March 2000 and April 2001. Diatom species composition was related to water quality parameters using multivariate statistics. 338 diatom species were identified. The seven most abundant species from pooled samples were Cocconeis placentula, Brachysira aponina, Nitzschia liebetruthii, Hyalosynedra laevigata, Amphora cf. tenerrima, Mastogloia crucicula, and M. pusilla. These seven species collectively accounted for 51.7 percent of all valves counted and occurred in at least 85 percent of all samples. Analysis of similiarity and NMDS ordination of species relative abundances revealed four distinct diatom communities across the study region. The spatial variability of these communities was correlated with salinity and water-column nutrient availability. Summertime communities were significantly different from winter-spring communities, but these communities showed a gradual temporal progression with much overlap. The temporal variability was correlated with temperature. Indicator species analysis identified many species significantly influencing the four spatial groups. The Atlantic marine site was characterized by many different Mastogloia species and some epipsammic (sand-grain associated) diatoms (i.e., Cymatosira lorenziana, Dimerogramma dubium, and Neofragilaria nicobarica). Mastogloia pusilla, Rhopalodia pacifica, and Cocconeis woodii were strong indicators of the Gulf of Mexico marine site. Reimerothrix floridensis was particularly abundant in the western interior of Florida Bay (i.e., sites 2, 3, and 4) during summer months. The eastern interior of Florida Bay was characterized by high relative abundances of Brachysira aponina and Nitzschia liebetruthii. The optima and tolerance of these indicator species relative to individual water quality parameters were also determined.

Parallel Implementation of Triangular Cellular Automata for Computing Two-Dimensional Elastodynamic Response on Arbitrary Domains

NASA Astrophysics Data System (ADS)

Leamy, Michael J.; Springer, Adam C.

In this research we report parallel implementation of a Cellular Automata-based simulation tool for computing elastodynamic response on complex, two-dimensional domains. Elastodynamic simulation using Cellular Automata (CA) has recently been presented as an alternative, inherently object-oriented technique for accurately and efficiently computing linear and nonlinear wave propagation in arbitrarily-shaped geometries. The local, autonomous nature of the method should lead to straight-forward and efficient parallelization. We address this notion on symmetric multiprocessor (SMP) hardware using a Java-based object-oriented CA code implementing triangular state machines (i.e., automata) and the MPI bindings written in Java (MPJ Express). We use MPJ Express to reconfigure our existing CA code to distribute a domain's automata to cores present on a dual quad-core shared-memory system (eight total processors). We note that this message passing parallelization strategy is directly applicable to computer clustered computing, which will be the focus of follow-on research. Results on the shared memory platform indicate nearly-ideal, linear speed-up. We conclude that the CA-based elastodynamic simulator is easily configured to run in parallel, and yields excellent speed-up on SMP hardware.

"Fabrication of arbitrarily shaped carbonate apatite foam based on the interlocking process of dicalcium hydrogen phosphate dihydrate".

PubMed

Sugiura, Yuki; Tsuru, Kanji; Ishikawa, Kunio

2017-08-01

Carbonate apatite (CO 3 Ap) foam with an interconnected porous structure is highly attractive as a scaffold for bone replacement. In this study, arbitrarily shaped CO 3 Ap foam was formed from α-tricalcium phosphate (α-TCP) foam granules via a two-step process involving treatment with acidic calcium phosphate solution followed by hydrothermal treatment with NaHCO 3 . The treatment with acidic calcium phosphate solution, which is key to fabricating arbitrarily shaped CO 3 Ap foam, enables dicalcium hydrogen phosphate dihydrate (DCPD) crystals to form on the α-TCP foam granules. The generated DCPD crystals cause the α-TCP granules to interlock with each other, inducing an α-TCP/DCPD foam. The interlocking structure containing DCPD crystals can survive hydrothermal treatment with NaHCO 3 . The arbitrarily shaped CO 3 Ap foam was fabricated from the α-TCP/DCPD foam via hydrothermal treatment at 200 °C for 24 h in the presence of a large amount of NaHCO 3 .

Growth rate and size effect on carbon isotopic fractionation in diatom-bound organic matter in recent Southern Ocean sediments

NASA Astrophysics Data System (ADS)

Stoll, Heather M.; Mendez-Vicente, Ana; Abrevaya, Lorena; Anderson, Robert F.; Rigual-Hernández, Andrés S.; Gonzalez-Lemos, Saul

2017-01-01

Carbon isotopic fractionation during photosynthesis (εp) is used to reconstruct past CO2 and phytoplankton growth rates, typically by measuring the δ13C of biomarkers produced by coccolithophorids. However, organic molecules bound within diatom frustules represent another phase for measurement of δ13C and offer the opportunity to obtain εp for specific diatom sizes and geometries. Here, from core top sediments covering a strong productivity gradient in the Southern Ocean, we present determinations of δ13C and εp from frustule-bound organic matter from a fine opal fraction dominated by pennate diatoms and a coarse opal fraction dominated by larger centric diatoms. The δ13C of the pennate diatom fraction is typically 2.8‰ more positive than that of the centric fraction. Both fractions show a comparable range of 9-10‰ over the core top transect. εp is lowest (6.3‰ in pennate fraction) between the Polar Front (PF) and Southern Antarctic Circumpolar Current Front (SACCF) and increases both to the north and south, with maximum values at greatest distance from the PF (18‰ in the pennate fraction). These spatial changes in εp are too large to arise from the rather modest variation in dissolved CO2 in surface waters across the core top transect. We suggest instead that the maximum εp reflects higher diatom growth rates, and in the case of pennate diatom F. kerguelensis also an increase in the frustule width and volume to surface area ratio. Both processes may result from enhanced Fe supply due to upwelling of circumpolar deep water between the PF and SACCF. Farther south, diatom growth is strongly Fe-limited and farther north it is Fe and Si co-limited. The optima of growth rates between the PF and SACCF appears to be a general feature in all sectors of the Southern Ocean. Such growth rate-induced changes in diatom εp allow us to resolve a 5° northward displacement of the PF during glacial times compared to interglacial times. By estimating CO2 aq in equilibrium with the Holocene ice core atmospheric CO2 concentrations, we quantify this growth rate effect and document that it is strongly correlated with indicators of trace metal supply, such as frustule Zn content, as well as indicators of diatom productivity such as opal % and opal accumulation rates in sediments and sediment traps. These relationships may be applied to constrain the effect of growth rate variations on εp and more accurately derive CO2 variations from εp during periods prior to ice core CO2 proxy records.

Do diatoms run downhill? Using biodiversity of terrestrial and aquatic diatoms to identify hydrological connectivity between aquatic zones in Luxembourg

NASA Astrophysics Data System (ADS)

Pfister, L.; Wetzel, C. E.; Martinez-Carreras, N.; Frentress, J.; Ector, L.; Hoffmann, L.; McDonnell, J. J.

2011-12-01

Diatoms are siliceous unicellular algae, and range in size between a few and more than 500 micrometers. Diatoms are spread worldwide, live in many aquatic habitats, have many life forms and their short generation time make them respond rapidly to environmental changes. Their taxonomic diversity represents a valuable tool to assess water quality as each taxon has specific responses to environmental factors. Recently, diatoms have been used as tracers to detect the onset/cessation of surface runoff through binary classification of terrestrial and aquatic species in the Attert basin in Luxembourg. In order to continue the validation of these first results, we have collected samples during rain events at different seasons of the year using automatic stream water samplers, grab samples of diatoms from various terrestrial and subaerial substrates (bryophytes, litter and leaves), as well as from aquatic habitats (epilithon, epipelon and drift samples). This new type of information will be used to constrain assumptions of the conventional tracer-based hydrograph separation technique (i.e. using geochemistry and stable isotopes). The first results concerning the diatom flora, based on 39 samples, revealed 152 species belonging to 38 genera. The most species-rich genera were Pinnularia (15.8% - 24 taxa), Eunotia (13.2% - 20 taxa), Gomphonema (8.6% - 13 taxa), Navicula (7.2% - 11 taxa) and Stauroneis (5.3% - 8 taxa). The flora are mainly composed of oligotrophic and/or acidophilic taxa (32.0%), ubiquitous (14.0%) or poorly known ecologically species (43.0%). The most important taxa found in drift samples were Fragilariforma virescens, Fragilaria capucina sensu lato, Planothidium lanceolatum, Eunotia minor, Achnanthidium kranzii, Karayevia oblongella and Eunotia incisa. In the riparian zone (n = 10), 102 species were observed, with Eunotia exigua var. tenella, Eunotia botuliformis and Pinnularia perirrorata being among the most frequent. Epilithic samples from the main channel have been represented mainly by monoraphid species such as Achnanthidium subatomoides and Achnanthidium minutissimum. A general qualitative overview of the diatom flora - concerning specific ecological requirements of the taxa - showed that most diatom species are characteristic of the riparian zone (30%), while 12% are typical of the riparian/upland transition zone. Only 3% of species are strictly freshwater (Aquatic zone) forms and 8% stem from the aquatic/riparian zone. The qualitative analysis of drift collected by automatic samplers showed that during floods the origin of diatom species partly stems from riparian and/or terrestrial-upland habitats. Additional investigations over a longer period and range of events are being conducted. Furthermore, the study of the biodiversity of diatoms in this small catchment will also contribute to a better definition of the ecological preferences of many species which are still poorly known to date.

Robustness of the filamentation instability as shock mediator in arbitrarily oriented magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bret, A.; Alvaro, E. Perez

2011-08-15

The filamentation instability (sometimes also referred to as ''Weibel'') is a key process in many astrophysical scenario. In the Fireball model for gamma ray bursts, this instability is believed to mediate collisionless shock formation from the collision of two plasma shells. It has been known for long that a flow aligned magnetic field can completely cancel this instability. We show here that in the general case where there is an angle between the field and the flow, the filamentation instability can never be stabilized, regardless of the field strength. The presented model analyzes the stability of two symmetric counter-streaming coldmore » electron/proton plasma shells. Relativistic effects are accounted for, and various exact analytical results are derived. This result guarantees the occurrence of the instability in realistic settings fulfilling the cold approximation.« less

Modelling UV irradiances on arbitrarily oriented surfaces: effects of sky obstructions

NASA Astrophysics Data System (ADS)

Hess, M.; Koepke, P.

2008-02-01

A method is presented to calculate UV irradiances on inclined surfaces that additionally takes into account the influence of sky obstructions caused by obstacles such as mountains, houses, trees, or umbrellas. Thus the method allows calculating the impact of UV radiation on biological systems, such as for instance the human skin or eye, in any natural or artificial environment. The method, a combination of radiation models, is explained and the correctness of its results is demonstrated. The effect of a natural skyline is shown for an Alpine ski area, where the UV irradiance even on a horizontal surface may increase due to reflection at snow by more than 10%. In contrast in a street canyon the irradiance on a horizontal surface is reduced down to 30% in shadow and to about 75% for a position in the sun.

Bubble collisions and measures of the multiverse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salem, Michael P., E-mail: salem@cosmos.phy.tufts.edu

2012-01-01

To compute the spectrum of bubble collisions seen by an observer in an eternally-inflating multiverse, one must choose a measure over the diverging spacetime volume, including choosing an ''initial'' hypersurface below which there are no bubble nucleations. Previous calculations focused on the case where the initial hypersurface is pushed arbitrarily deep into the past. Interestingly, the observed spectrum depends on the orientation of the initial hypersurface, however one's ability observe the effect rapidly decreases with the ratio of inflationary Hubble rates inside and outside one's bubble. We investigate whether this conclusion might be avoided under more general circumstances, including placingmore » the observer's bubble near the initial hypersurface. We find that it is not. As a point of reference, a substantial appendix reviews relevant aspects of the measure problem of eternal inflation.« less

Scattering from arbitrarily shaped microstrip patch antennas

NASA Technical Reports Server (NTRS)

Shively, David G.; Deshpande, Manohar D.; Cockrell, Capers R.

1992-01-01

The scattering properties of arbitrarily shaped microstrip patch antennas are examined. The electric field integral equation for a current element on a grounded dielectric slab is developed for a rectangular geometry based on Galerkin's technique with subdomain rooftop basis functions. A shape function is introduced that allows a rectangular grid approximation to the arbitrarily shaped patch. The incident field on the patch is expressed as a function of incidence angle theta(i), phi(i). The resulting system of equations is then solved for the unknown current modes on the patch, and the electromagnetic scattering is calculated for a given angle. Comparisons are made with other calculated results as well as with measurements.

Calibration of an arbitrarily arranged projection moiré system for 3D shape measurement

NASA Astrophysics Data System (ADS)

Tang, Ying; Yao, Jun; Zhou, Yihao; Sun, Chen; Yang, Peng; Miao, Hong; Chen, Jubing

2018-05-01

An arbitrarily arranged projection moiré system is presented for three-dimensional shape measurement. We develop a model for projection moiré system and derive a universal formula expressing the relation between height and phase variation before and after we put the object on the reference plane. With so many system parameters involved, a system calibration technique is needed. In this work, we provide a robust and accurate calibration method for an arbitrarily arranged projection moiré system. The system no longer puts restrictions on the configuration of the optical setup. Real experiments have been conducted to verify the validity of this method.

Nonlinear vibrations of thin arbitrarily laminated composite plates subjected to harmonic excitations using DKT elements

NASA Astrophysics Data System (ADS)

Chiang, C. K.; Xue, David Y.; Mei, Chuh

1993-04-01

A finite element formulation is presented for determining the large-amplitude free and steady-state forced vibration response of arbitrarily laminated anisotropic composite thin plates using the Discrete Kirchhoff Theory (DKT) triangular elements. The nonlinear stiffness and harmonic force matrices of an arbitrarily laminated composite triangular plate element are developed for nonlinear free and forced vibration analyses. The linearized updated-mode method with nonlinear time function approximation is employed for the solution of the system nonlinear eigenvalue equations. The amplitude-frequency relations for convergence with gridwork refinement, triangular plates, different boundary conditions, lamination angles, number of plies, and uniform versus concentrated loads are presented.

Nonlinear vibrations of thin arbitrarily laminated composite plates subjected to harmonic excitations using DKT elements

NASA Technical Reports Server (NTRS)

Chiang, C. K.; Xue, David Y.; Mei, Chuh

1993-01-01

A finite element formulation is presented for determining the large-amplitude free and steady-state forced vibration response of arbitrarily laminated anisotropic composite thin plates using the Discrete Kirchhoff Theory (DKT) triangular elements. The nonlinear stiffness and harmonic force matrices of an arbitrarily laminated composite triangular plate element are developed for nonlinear free and forced vibration analyses. The linearized updated-mode method with nonlinear time function approximation is employed for the solution of the system nonlinear eigenvalue equations. The amplitude-frequency relations for convergence with gridwork refinement, triangular plates, different boundary conditions, lamination angles, number of plies, and uniform versus concentrated loads are presented.

The insidious effect of diatoms on copepod reproduction

NASA Astrophysics Data System (ADS)

Miralto, A.; Barone, G.; Romano, G.; Poulet, S. A.; Ianora, A.; Russo, G. L.; Buttino, I.; Mazzarella, G.; Laabir, M.; Cabrini, M.; Giacobbe, M. G.

1999-11-01

The productive regions of the ocean are characterized by seasonal blooms of phytoplankton which are generally dominated by diatoms. This algal class has, therefore, traditionally been regarded as providing the bulk of the food that sustains the marine food chain to top consumers and important fisheries. However, this beneficial role has recently been questioned on the basis of laboratory studies showing that although dominant zooplankton grazers such as copepods feed extensively on diatoms, the hatching success of eggs thus produced is seriously impaired. Here we present evidence from the field showing that the hatching success of wild copepods feeding on a diatom-dominated bloom is also heavily compromised, with only 12% of the eggs hatching compared with 90% in post-bloom conditions. We report on the structure of the three aldehydes isolated from diatoms that are responsible for this biological activity, and show that these compounds arrest embryonic development in copepod and sea urchin bioassays and have antiproliferative and apoptotic effects on human carcinoma cells.

Freshwater monsoon related inputs in the Japan Sea: a diatom record from IODP core U1427

NASA Astrophysics Data System (ADS)

Ventura, C. P. L.; Lopes, C.

2016-12-01

Monsoon rainfall is the life-blood of more than half the world's population. Extensive research is being conducted in order to refine projections regarding the impact of anthropogenic climate change on these systems. The East Asian monsoon (EAM) plays a significant role in large-scale climate variability. Due to its importance to global climate and world's population, there is an urgent need for greater understanding of this system, especially during past climate changes. The input of freshwater from the monsoon precipitation brings specific markers, such as freshwater diatoms and specific diatom ecological assemblages that are preserved in marine sediments. Freshwater diatoms are easily identifiable and have been used in the North Pacific to reconstruct environmental conditions (Lopes et al 2006) and flooding episodes (Lopes and Mix, 2009). Here we show preliminary results of freshwater diatoms records that are linked with river discharge due to increase land rainfall that can be derived from Monsoon rainfall. We extend our preliminary study to the past 400ky.

X-ray fluorescence mapping of mercury on suspended mineral particles and diatoms in a contaminated freshwater system

NASA Astrophysics Data System (ADS)

Gu, B.; Mishra, B.; Miller, C.; Wang, W.; Lai, B.; Brooks, S. C.; Kemner, K. M.; Liang, L.

2014-09-01

Mercury (Hg) bioavailability and geochemical cycling is affected by its partitioning between the aqueous and particulate phases. We applied a synchrotron-based X-ray fluorescence (XRF) microprobe to visualize and quantify directly the spatial localization of Hg and its correlations with other elements of interest on suspended particles from a Hg-contaminated freshwater system. Up to 175 μg g-1 Hg is found on suspended particles, but less than 0.01% is in the form of methylmercury. Mercury is heterogeneously distributed among phytoplankton (e.g., diatoms) and mineral particles that are rich in iron oxides and natural organic matter (NOM). The diatom-bound Hg is mostly found on outer surfaces of the cells, suggesting passive sorption of Hg on diatoms. Our results indicate that localized sorption of Hg onto suspended particles, including diatoms and NOM-coated oxide minerals, may play an important role in affecting the partitioning, reactivity, and biogeochemical cycling of Hg in natural aquatic environments.

Diatom Derived Polyunsaturated Aldehydes Do Not Structure the Planktonic Microbial Community in a Mesocosm Study

PubMed Central

Paul, Carsten; Reunamo, Anna; Lindehoff, Elin; Bergkvist, Johanna; Mausz, Michaela A.; Larsson, Henrik; Richter, Hannes; Wängberg, Sten-Åke; Leskinen, Piia; Båmstedt, Ulf; Pohnert, Georg

2012-01-01

Several marine and freshwater diatoms produce polyunsaturated aldehydes (PUA) in wound-activated processes. These metabolites are also released by intact diatom cells during algal blooms. Due to their activity in laboratory experiments, PUA are considered as potential mediators of diatom-bacteria interactions. Here, we tested the hypothesis that PUA mediate such processes in a close-to-field mesocosm experiment. Natural plankton communities enriched with Skeletonema marinoi strains that differ in their PUA production, a plankton control, and a plankton control supplemented with PUA at natural and elevated concentrations were observed. We monitored bacterial and viral abundance as well as bacterial community composition and did not observe any influence of PUA on these parameters even at elevated concentrations. We rather detected an alternation of the bacterial diversity over time and differences between the two S. marinoi strains, indicating unique dynamic bacterial communities in these algal blooms. These results suggest that factors other than PUA are of significance for interactions between diatoms and bacteria. PMID:22690143

Critical nitrogen deposition loads in high-elevation lakes of the western US inferred from paleolimnological records

USGS Publications Warehouse

Saros, J.E.; Clow, D.W.; Blett, T.; Wolfe, A.P.

2011-01-01

Critical loads of nitrogen (N) from atmospheric deposition were determined for alpine lake ecosystems in the western US using fossil diatom assemblages in lake sediment cores. Changes in diatom species over the last century were indicative of N enrichment in two areas, the eastern Sierra Nevada, starting between 1960 and 1965, and the Greater Yellowstone Ecosystem, starting in 1980. In contrast, no changes in diatom community structure were apparent in lakes of Glacier National Park. To determine critical N loads that elicited these community changes, we modeled wet nitrogen deposition rates for the period in which diatom shifts first occurred in each area using deposition data spanning from 1980 to 2007. We determined a critical load of 1.4 kg N ha-1 year-1 wet N deposition to elicit key nutrient enrichment effects on diatom communities in both the eastern Sierra Nevada and the Greater Yellowstone Ecosystem. ?? 2010 Springer Science+Business Media B.V.

Study of the mechanism of diatom cell division by means of 29Si isotope tracing

NASA Astrophysics Data System (ADS)

Audinot, J.-N.; Guignard, C.; Migeon, H.-N.; Hoffmann, L.

2006-07-01

Diatoms are delicate unicellular organisms enclosed in a silica frustule, that is made up of two valves. Multiplication of the diatoms occurs by ordinary mitotic cell division. During cell division each cell produces two daughter cells, each of them keeping one of the two valves of the mother cell and producing a new valve by absorbing the silicon present in the environment. The NanoSIMS 50 allows ion imaging to be performed on diatoms in order to determine the site of fixation of silicon. The aim of this study was to observe and compare the mechanism of the construction of the new valve after cell division. To this end, different types of diatoms have been transferred in a culture medium enriched with 29Si and after several days, the distribution of the different isotopes of silicon has been determined by NanoSIMS50 imaging. The construction of new valves has been observed and the isotopic ratio has been determined.

Diatoms Si uptake capacity drives carbon export in coastal upwelling systems

NASA Astrophysics Data System (ADS)

Abrantes, Fatima; Cermeno, Pedro; Lopes, Cristina; Romero, Oscar; Matos, Lélia; Van Iperen, Jolanda; Rufino, Marta; Magalhães, Vitor

2016-07-01

Coastal upwelling systems account for approximately half of global ocean primary production and contribute disproportionately to biologically driven carbon sequestration. Diatoms, silica-precipitating microalgae, constitute the dominant phytoplankton in these productive regions, and their abundance and assemblage composition in the sedimentary record is considered one of the best proxies for primary production. The study of the sedimentary diatom abundance (SDA) and total organic carbon content (TOC) in the five most important coastal upwelling systems of the modern ocean (Iberia-Canary, Benguela, Peru-Humboldt, California, and Somalia-Oman) reveals a global-scale positive relationship between diatom production and organic carbon burial. The analysis of SDA in conjunction with environmental variables of coastal upwelling systems such as upwelling strength, satellite-derived net primary production, and surface water nutrient concentrations shows different relations between SDA and primary production on the regional scale. On the global scale, SDA appears modulated by the capacity of diatoms to take up silicic acid, which ultimately sets an upper limit to global export production in these ocean regions.

Phytoplankton community indicators of changes associated with dredging in the Tagus estuary (Portugal).

PubMed

Cabrita, Maria Teresa

2014-08-01

This work reports changes in suspended particulate matter, turbidity, dissolved Cr, Ni, Cu, Cd, Hg and Pb concentrations, and phytoplankton biomass and composition during a 5-month period dredging operation, in a trace element contaminated area of the Tagus estuary (Portugal). Phytoplankton biomass, diatom:other groups ratio, benthic:pelagic diatom ratio, Margalef's, Simpson's diversity, Shannon-Wiever's, and Warwick and Clarke's taxonomic diversity and distinctness indices, and individual taxa were investigated as indicators of dredging induced changes. Significant rise in sediment resuspension and trace element mobilisation caused by dredging influenced the community structure but not the overall biomass. Benthic diatom displacement into the water column maintained species diversity, and therefore, none of the indices highlighted community changes. Contrastingly, diatom:other groups ratio and benthic:pelagic diatom ratio were reliable indicators for the assessment of dredging induced changes. A shift in composition towards species less susceptible to trace elements was observed, disclosing some individual taxa as potential indicators. Copyright © 2014 Elsevier Ltd. All rights reserved.

A sex-inducing pheromone triggers cell cycle arrest and mate attraction in the diatom Seminavis robusta

PubMed Central

Moeys, Sara; Frenkel, Johannes; Lembke, Christine; Gillard, Jeroen T. F.; Devos, Valerie; Van den Berge, Koen; Bouillon, Barbara; Huysman, Marie J. J.; De Decker, Sam; Scharf, Julia; Bones, Atle; Brembu, Tore; Winge, Per; Sabbe, Koen; Vuylsteke, Marnik; Clement, Lieven; De Veylder, Lieven; Pohnert, Georg; Vyverman, Wim

2016-01-01

Although sexual reproduction is believed to play a major role in the high diversification rates and species richness of diatoms, a mechanistic understanding of diatom life cycle control is virtually lacking. Diatom sexual signalling is controlled by a complex, yet largely unknown, pheromone system. Here, a sex-inducing pheromone (SIP+) of the benthic pennate diatom Seminavis robusta was identified by comparative metabolomics, subsequently purified, and physicochemically characterized. Transcriptome analysis revealed that SIP+ triggers the switch from mitosis-to-meiosis in the opposing mating type, coupled with the transcriptional induction of proline biosynthesis genes, and the release of the proline-derived attraction pheromone. The induction of cell cycle arrest by a pheromone, chemically distinct from the one used to attract the opposite mating type, highlights the existence of a sophisticated mechanism to increase chances of mate finding, while keeping the metabolic losses associated with the release of an attraction pheromone to a minimum. PMID:26786712

X-ray fluorescence mapping of mercury on suspended mineral particles and diatoms in a contaminated freshwater system

DOE PAGES

Gu, Baohua; Mishra, Bhoopesh; Miller, Carrie L.; ...

2014-01-01

Mercury (Hg) bioavailability and geochemical cycling is affected by its partitioning between the aqueous and particulate phases. We applied a synchrotron-based X-ray fluorescence (XRF) microprobe to visualize and quantify directly the spatial localization of Hg and its correlations with other elements of interest on suspended particles from a Hg-contaminated freshwater system. Up to 175 μg g −1 Hg is found on suspended particles, but less than 0.01% is in the form of methylmercury. Mercury is heterogeneously distributed among phytoplankton (e.g., diatoms) and mineral particles that are rich in iron oxides and natural organic matter (NOM). The diatom-bound Hg is mostlymore » found on outer surfaces of the cells, suggesting passive sorption of Hg on diatoms. Our results indicate that localized sorption of Hg onto suspended particles, including diatoms and NOM-coated oxide minerals, may play an important role in affecting the partitioning, reactivity, and biogeochemical cycling of Hg in natural aquatic environments.« less

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

DOE PAGES

Diner, Rachel E.; Noddings, Chari M.; Lian, Nathan C.; ...

2017-07-18

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequencemore » features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.« less

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diner, Rachel E.; Noddings, Chari M.; Lian, Nathan C.

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequencemore » features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.« less

Disentangling diatom species complexes: does morphometry suffice?

PubMed Central

Borrego-Ramos, María; Olenici, Adriana

2017-01-01

Accurate taxonomic resolution in light microscopy analyses of microalgae is essential to achieve high quality, comparable results in both floristic analyses and biomonitoring studies. A number of closely related diatom taxa have been detected to date co-occurring within benthic diatom assemblages, sharing many morphological, morphometrical and ecological characteristics. In this contribution, we analysed the hypothesis that, where a large sample size (number of individuals) is available, common morphometrical parameters (valve length, width and stria density) are sufficient to achieve a correct identification to the species level. We focused on some common diatom taxa belonging to the genus Gomphonema. More than 400 valves and frustules were photographed in valve view and measured using Fiji software. Several statistical tools (mixture and discriminant analysis, k-means clustering, classification trees, etc.) were explored to test whether mere morphometry, independently of other valve features, leads to correct identifications, when compared to identifications made by experts. In view of the results obtained, morphometry-based determination in diatom taxonomy is discouraged. PMID:29250472

The effects of phosphorus limitation on carbon metabolism in diatoms.

PubMed

Brembu, Tore; Mühlroth, Alice; Alipanah, Leila; Bones, Atle M

2017-09-05

Phosphorus is an essential element for life, serving as an integral component of nucleic acids, lipids and a diverse range of other metabolites. Concentrations of bioavailable phosphorus are low in many aquatic environments. Microalgae, including diatoms, apply physiological and molecular strategies such as phosphorus scavenging or recycling as well as adjusting cell growth in order to adapt to limiting phosphorus concentrations. Such strategies also involve adjustments of the carbon metabolism. Here, we review the effect of phosphorus limitation on carbon metabolism in diatoms. Two transcriptome studies are analysed in detail, supplemented by other transcriptome, proteome and metabolite data, to gain an overview of different pathways and their responses. Phosphorus, nitrogen and silicon limitation responses are compared, and similarities and differences discussed. We use the current knowledge to propose a suggestive model for the carbon flow in phosphorus-replete and phosphorus-limited diatom cells.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Authors.

Stuart R. Stidolph diatom atlas

USGS Publications Warehouse

Stidolph, S.R.; Sterrenburg, F.A.S.; Smith, K.E.L.; Kraberg, A.

2012-01-01

The "Stuart R. Stidolph Diatom Atlas" is a comprehensive volume of diatom taxa identified and micrographed by Stuart R. Stidoph during the 1980s and 1990s. The samples were collected from marine coasts of various geographic regions within tropical and subtropical climates. The plates included within this report have never been published and are being published by the USGS as an online reference so that others may have access to this incredible collection.

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria

NASA Astrophysics Data System (ADS)

Amin, S. A.; Hmelo, L. R.; van Tol, H. M.; Durham, B. P.; Carlson, L. T.; Heal, K. R.; Morales, R. L.; Berthiaume, C. T.; Parker, M. S.; Djunaedi, B.; Ingalls, A. E.; Parsek, M. R.; Moran, M. A.; Armbrust, E. V.

2015-06-01

Interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape ecosystem diversity. In marine ecosystems, these interactions are difficult to study partly because the major photosynthetic organisms are microscopic, unicellular phytoplankton. Coastal phytoplankton communities are dominated by diatoms, which generate approximately 40% of marine primary production and form the base of many marine food webs. Diatoms co-occur with specific bacterial taxa, but the mechanisms of potential interactions are mostly unknown. Here we tease apart a bacterial consortium associated with a globally distributed diatom and find that a Sulfitobacter species promotes diatom cell division via secretion of the hormone indole-3-acetic acid, synthesized by the bacterium using both diatom-secreted and endogenous tryptophan. Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia. The potential prevalence of this mode of signalling in the oceans is corroborated by metabolite and metatranscriptome analyses that show widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal environments. Our study expands on the emerging recognition that marine microbial communities are part of tightly connected networks by providing evidence that these interactions are mediated through production and exchange of infochemicals.

Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta).

PubMed

Nakov, Teofil; Beaulieu, Jeremy M; Alverson, Andrew J

2018-04-06

Patterns of species richness are commonly linked to life history strategies. In diatoms, an exceptionally diverse lineage of photosynthetic heterokonts important for global photosynthesis and burial of atmospheric carbon, lineages with different locomotory and reproductive traits differ dramatically in species richness, but any potential association between life history strategy and diversification has not been tested in a phylogenetic framework. We constructed a time-calibrated, 11-gene, 1151-taxon phylogeny of diatoms - the most inclusive diatom species tree to date. We used this phylogeny, together with a comprehensive inventory of first-last occurrences of Cenozoic fossil diatoms, to estimate ranges of expected species richness, diversification and its variation through time and across lineages. Diversification rates varied with life history traits. Although anisogamous lineages diversified faster than oogamous ones, this increase was restricted to a nested clade with active motility in the vegetative cells. We propose that the evolution of motility in vegetative cells, following an earlier transition from oogamy to anisogamy, facilitated outcrossing and improved utilization of habitat complexity, ultimately leading to enhanced opportunity for adaptive divergence across a variety of novel habitats. Together, these contributed to a species radiation that gave rise to the majority of present-day diatom diversity. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Reconstruction of vegetation and lake level at Moon Lake, North Dakota, from high-resolution pollen and diatom data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grimm, E.C.; Laird, K.R.; Mueller, P.G.

High-resolution fossil-pollen and diatom data from Moon Lake, North Dakota, reveal major climate and vegetation changes near the western margin of the tall-grass prairie. Fourteen AMS radiocarbon dates provide excellent time control for the past {approximately}11,800 {sup 14}C years B.P. Picea dominated during the late-glacial until it abruptly declined {approximately}10,300 B.P. During the early Holocene ({approximately}10,300-8000 B.P.), deciduous trees and shrubs (Populus, Betula, Corylus, Quercus, and especially Ulmus) were common, but prairie taxa (Poaceae, Artemisia, and Chenopodiaceae/Amaranthaceae) gradually increased. During this period the diatoms indicate the lake becoming gradually more saline as water-level fell. By {approximately}8000 B.P., salinity had increasedmore » to the point that the diatoms were no longer sensitive to further salinity increases. However, fluctuating pollen percentages of mud-flat weeds (Ambrosia and Iva) indicate frequently changing water levels during the mid-Holocene ({approximately}8000-5000 B.P.). The driest millennium was 7000-6000 B.P., when Iva annua was common. After {approximately}3000 B.P. the lake became less-saline, and the diatoms were again sensitive to changing salinity. The Medieval Warm Period and Little Ice Age are clearly evident in the diatom data.« less

Can we predict diatoms herbicide sensitivities with phylogeny? Influence of intraspecific and interspecific variability.

PubMed

Esteves, Sara M; Keck, François; Almeida, Salomé F P; Figueira, Etelvina; Bouchez, Agnès; Rimet, Frédéric

2017-10-01

Diatoms are used as indicators of freshwater ecosystems integrity. Developing diatom-based tools to assess impact of herbicide pollution is expected by water managers. But, defining sensitivities of all species to multiple herbicides would be unattainable. The existence of a phylogenetic signal of herbicide sensitivity was shown among diatoms and should enable prediction of new species sensitivity. However, diatoms present a cryptic diversity that may lead to variation in their sensitivity to herbicides that would need to be taken into account. Using bioassays, the sensitivity to four herbicides (Atrazine, Terbutryn, Diuron, Isoproturon) was evaluated for 11 freshwater diatom taxa and intraspecific variability was assessed for two of them (Nitzschia palea and Achnanthidium spp.). Intraspecific variability of herbicide sensitivity was always smaller than interspecific variability, but intraspecific variability was more important in N. palea than in Achnanthidium spp. Indeed, one species showed no intraspecific phylogenetic signal (N. palea) whereas the other did (Achnanthidium spp.). On one hand, species boundaries are not set properly for Achnanthidium spp. which encompass several taxa. On the other hand, there is a higher phenotypic plasticity for N. palea. Finally, a phylogenetic signal of herbicide sensitivity was measured at the interspecific level, opening up prospects for setting up reliable biomonitoring tools based on sensitivity prediction, insofar as species boundaries are correctly defined.

Amine-functionalized diatom frustules: a platform for specific and sensitive detection of nitroaromatic explosive derivative.

PubMed

Selvaraj, Viji; Thomas, Neethi; Anthuvan, Allen Joseph; Nagamony, Ponpandian; Chinnuswamy, Viswanathan

2017-12-14

In the present study, an attempt was made to develop a proof of concept for the detection of nitroaromatic explosive derivatives through the photoluminescence (PL) quenching process using functionalized diatom frustules as a sensing platform. The diatom frustules are composed of nanostructured, highly porous biogenic silica material and emit strong, visible blue PL upon UV excitation. PL-active biosilica was isolated from the marine diatom Nitzschia sp. and was amine-functionalized to develop a sensing platform. Functionalized diatom frustules were further characterized using field emission scanning electron microscope and a series of spectroscopic methods. When nitroaromatic compounds were bound to the functionalized diatom frustules biosilica, the PL intensity from the functionalized biosilica was partially quenched due to the electrophilic nature of the nitro (-NO) groups. The quenching process confirmed the Meisenheimer complex formation and was investigated by using Fourier transform infrared spectroscopy and time-resolved photoluminescence studies. The developed platform was further evaluated for its sensitivity and specificity, and the limit of detection (LOD) of the assay was determined as 1 μM for a series of nitroaromatic explosive compounds. In conclusion, the developed sensing platform will have great utility in the development of on-site detection platforms for sensitive detection of warfare explosive nitroaromatic compounds from the environment.

A comparative gene expression analysis of iron-limited cultures of Chaetoceros socialis and Pseudo-nitzschia arenysensis using newly developed iron assays

NASA Astrophysics Data System (ADS)

Abdala, Z. M.; Powell, K.; Cronin, D.; Chappell, D.

2016-02-01

A comparative gene expression analysis of iron-limited cultures of Chaetoceros socialis and Pseudo-nitzschia arenysensisusing newly developed iron assays Zuzanna M. Abdala, Kimberly Powell, Dylan P. Cronin, P. Dreux Chappell Diatoms, accounting for about 40% of the primary production in marine ecosystems, play a vital role in the dynamics of marine systems. Iron availability is understood to be a driving factor controlling productivity of many marine phytoplankton, including diatoms, as it functions as a cofactor for many proteins including several involved with photosynthetic processes. Previous work examining transcriptomes of diatoms of the Thalassiosira genus grown in controlled laboratory settings has identified genes whose expression can be used as sensitive markers of iron status. Data mining publically available diatom transcriptome data for these genes enables development of additional iron status assays for environmentally-relevant diatoms. For the present study, gene expression analysis of iron-limited laboratory cultures of Chaetoceros socialis and Pseudo-nitzschia arenysensis grown in continuous light was done using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). C. socialis and P. arenysensis serve as comparative models for analyzing gene expression in iron limitation in different ecological community assemblages. These data may ultimately assist to illuminate the function of iron in photosynthetic activity in diatoms.

Outdoor Cultivation of Marine Diatoms for Year-Round Production of Biofuels.

PubMed

Matsumoto, Mitsufumi; Nojima, Daisuke; Nonoyama, Tomomi; Ikeda, Kiichi; Maeda, Yoshiaki; Yoshino, Tomoko; Tanaka, Tsuyoshi

2017-03-25

Biofuel production using microalgae is believed to have the advantage of continuous year-round production over crop plants, which have strong seasonality. However, actual year-round production of microalgal lipids using outdoor mass cultivation has rarely been demonstrated. In our previous study, it was demonstrated that the oleaginous diatom, Fistulifera solaris , was culturable in outdoor bioreactors from spring to autumn, whereas biomass and lipid production in winter failed because F. solaris did not grow below 15 °C. Therefore, another candidate strain that is culturable in winter is required. In this study, a cold-tolerant diatom, Mayamaea sp. JPCC CTDA0820, was selected as a promising candidate for biofuel production in winter. Laboratory-scale characterization revealed that this diatom was culturable at temperatures as low as 10 °C. Subsequently, F. solaris (April-October) and Mayamaea sp. JPCC CTDA0820 (November-March) were cultured in outdoor open-pond bioreactors, wherein year-round production of diatom lipids was successfully demonstrated. The maximal values of areal productivities of biomass and lipids reached to 9.79 and 1.80 g/(m² day) for F. solaris , and 8.62 and 0.92 g/(m² day) for Mayamaea sp. JPCC CTDA0820, respectively. With the combined use of these two diatom species, stable year-round production of microalgal lipids became possible.

Direct versus indirect climate controls on Holocene diatom assemblages in a sub-tropical deep, alpine lake (Lugu Hu, Yunnan, SW China)

NASA Astrophysics Data System (ADS)

Wang, Qian; Yang, Xiangdong; Anderson, Nicholas John; Dong, Xuhui

2016-07-01

The reconstruction of Holocene environmental changes in lakes on the plateau region of southwest China provides an understanding of how these ecosystems may respond to climate change. Fossil diatom assemblages were investigated from an 11,000-year lake sediment core from a deep, alpine lake (Lugu Hu) in southwest China, an area strongly influenced by the southwest (or the Indian) summer monsoon. Changes in diatom assemblage composition, notably the abundance of the two dominant planktonic species, Cyclotella rhomboideo-elliptica and Cyclostephanos dubius, reflect the effects of climate variability on nutrient dynamics, mediated via thermal stratification (internal nutrient cycling) and catchment-vegetation processes. Statistical analyses of the climate-diatom interactions highlight the strong effect of changing orbitally-induced solar radiation during the Holocene, presumably via its effect on the lake's thermal budget. In a partial redundancy analysis, climate (solar insolation) and proxies reflecting catchment process (pollen percentages, C/N ratio) were the most important drivers of diatom ecological change, showing the strong effects of climate-catchment-vegetation interactions on lake functioning. This diatom record reflects long-term ontogeny of the lake-catchment ecosystem and suggests that climatic changes (both temperature and precipitation) impact lake ecology indirectly through shifts in thermal stratification and catchment nutrient exports.

Genome-Wide Transcriptome Analyses of Silicon Metabolism in Phaeodactylum tricornutum Reveal the Multilevel Regulation of Silicic Acid Transporters

PubMed Central

Sapriel, Guillaume; Quinet, Michelle; Heijde, Marc; Jourdren, Laurent; Tanty, Véronique; Luo, Guangzuo; Le Crom, Stéphane; Lopez, Pascal Jean

2009-01-01

Background Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)4 can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles. Methodology/Principal Findings Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations. Conclusions/Significance Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins. PMID:19829693

Diatoms on the carapace of common snapping turtles: Luticola spp. dominate despite spatial variation in assemblages

PubMed Central

Wu, Shelly C.; Bergey, Elizabeth A.

2017-01-01

Filamentous algae are often visible on the carapaces of freshwater turtles and these algae are dominated by a few species with varying geographic distributions. Compared to filamentous algae, little is known about the much more speciose microalgae on turtles. Our objectives were to compare the diatom flora on a single turtle species (the common snapping turtle, Chelydra serpentina) across part of its range to examine spatial patterns and determine whether specific diatom taxa were consistently associated with turtles (as occurs in the filamentous alga Basicladia spp.). Using preserved turtle specimens from museums, we systematically sampled diatoms on the carapaces of 25 snapping turtles across five states. The diverse diatom assemblages formed two groups–the southern Oklahoma group and the northern Illinois/Wisconsin/New York group, with Arkansas not differing from either group. Of the six diatom species found in all five states, four species are widespread, whereas Luticola cf. goeppertiana and L. cf. mutica are undescribed species, known only from turtles in our study. L. cf. goeppertiana comprised 83% of the diatom abundance on Oklahoma turtles and was relatively more abundant on southern turtles (Oklahoma and Arkansas) than on northern turtles (where mean abundance/state was > 10%). L. cf. mutica was the most abundant species (40%) on New York turtles. Some Luticola species are apparently turtle associates and results support a pattern of spatial variation in Luticola species, similar to that in Basicladia. Using museum specimens is an efficient and effective method to study the distribution of micro-epibionts. PMID:28192469

An evaluation of restoration efforts in fishless lakes stocked with exotic trout

USGS Publications Warehouse

Drake, D.C.; Naiman, R.J.

2000-01-01

Detrimental effects of introduced fishes on native amphibian populations have prompted removal of introduced cutthroat (Oncorhynchus clarki), rainbow (Oncorhynchus mykiss), and brook trout (Salvelinus fontinalis) from naturally fishless lakes at Mt. Rainier National Park, Washington (U.S.A.). Using paleolimnological indicators (diatoms, invertebrates, and sediment characteristics) in eight 480-year-old sediment cores from eight lakes, we (1) derived estimates of baseline environmental conditions and natural variation, (2) assessed the effects of stocking naturally fishless lakes, and (3) determined whether lakes returned to predisturbance conditions after fish removal (restoration). Diatom floras were relatively stable between 315 and 90 years before present in all lakes; we used this time period to define lake-specific "baseline" conditions. Dissimilarity analyses of diatoms revealed sustained, dramatic changes in diatom floras that occurred approximately 80 years ago (when fish were introduced) in four of five stocked lakes, whereas the diatom floras in two unstocked lakes had not changed significantly in the last 315 years. Diatoms were not preserved in an eighth lake. State changes also occurred in two lakes over 200 years before European settlement of the Pacific Northwest. Preserved invertebrate densities fluctuated dramatically over time in all cores, providing a poor reference for assessing the effects of fishes. Nevertheless, fish-invertebrate interactions have been demonstrated in other paleolimnological studies and may be useful for lower-elevation or more productive lakes. Because diatom communities have not returned to predisturbance assemblages in restored lakes, even 20-30 years after fish removal, we conclude that Mt. Rainier lakes were not successfully restored by the removal of fishes.

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula.

PubMed

Pearson, Gareth A; Lago-Leston, Asuncion; Cánovas, Fernando; Cox, Cymon J; Verret, Frederic; Lasternas, Sebastian; Duarte, Carlos M; Agusti, Susana; Serrão, Ester A

2015-10-01

Functional genomics of diatom-dominated communities from the Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded more than 500K pyrosequencing reads that were combined to produce a global metatranscriptome assembly. Multi-gene phylogenies recovered three distinct communities, and diatom-assigned contigs further indicated little read-sharing between communities, validating an assembly-based annotation and analysis approach. Although functional analysis recovered a core of abundant shared annotations that were expressed across the three diatom communities, over 40% of annotations (but accounting for <10% of sequences) were community-specific. The two pelagic communities differed in their expression of N-metabolism and acquisition genes, which was almost absent in post-bloom conditions in the Weddell Sea community, while enrichment of transporters for ammonia and urea in Bransfield Strait diatoms suggests a physiological stance towards acquisition of reduced N-sources. The depletion of carbohydrate and energy metabolism pathways in sea ice relative to pelagic communities, together with increased light energy dissipation (via LHCSR proteins), photorespiration, and NO3(-) uptake and utilization all pointed to irradiance stress and/or inorganic carbon limitation within sea ice. Ice-binding proteins and cold-shock transcription factors were also enriched in sea ice diatoms. Surprisingly, the abundance of gene transcripts for the translational machinery tracked decreasing environmental temperature across only a 4 °C range, possibly reflecting constraints on translational efficiency and protein production in cold environments.

Diatoms on the carapace of common snapping turtles: Luticola spp. dominate despite spatial variation in assemblages.

PubMed

Wu, Shelly C; Bergey, Elizabeth A

2017-01-01

Filamentous algae are often visible on the carapaces of freshwater turtles and these algae are dominated by a few species with varying geographic distributions. Compared to filamentous algae, little is known about the much more speciose microalgae on turtles. Our objectives were to compare the diatom flora on a single turtle species (the common snapping turtle, Chelydra serpentina) across part of its range to examine spatial patterns and determine whether specific diatom taxa were consistently associated with turtles (as occurs in the filamentous alga Basicladia spp.). Using preserved turtle specimens from museums, we systematically sampled diatoms on the carapaces of 25 snapping turtles across five states. The diverse diatom assemblages formed two groups-the southern Oklahoma group and the northern Illinois/Wisconsin/New York group, with Arkansas not differing from either group. Of the six diatom species found in all five states, four species are widespread, whereas Luticola cf. goeppertiana and L. cf. mutica are undescribed species, known only from turtles in our study. L. cf. goeppertiana comprised 83% of the diatom abundance on Oklahoma turtles and was relatively more abundant on southern turtles (Oklahoma and Arkansas) than on northern turtles (where mean abundance/state was > 10%). L. cf. mutica was the most abundant species (40%) on New York turtles. Some Luticola species are apparently turtle associates and results support a pattern of spatial variation in Luticola species, similar to that in Basicladia. Using museum specimens is an efficient and effective method to study the distribution of micro-epibionts.

Effects of the oxylipin-producing diatom Skeletonema marinoi on gene expression levels of the calanoid copepod Calanus sinicus.

PubMed

Lauritano, Chiara; Carotenuto, Ylenia; Vitiello, Valentina; Buttino, Isabella; Romano, Giovanna; Hwang, Jiang-Shiou; Ianora, Adrianna

2015-12-01

Diatoms are eukaryotic unicellular plants that constitute one of the major components of marine phytoplankton, comprising up to 40% of annual productivity at sea and representing 25% of global carbon-fixation. Diatoms have traditionally been considered a preferential food for zooplankton grazers such as copepods, but, in the last two decades, this beneficial role has been challenged after the discovery that many species of diatoms produce toxic metabolites, collectively termed oxylipins, that induce reproductive failure in zooplankton grazers. Diatoms are the dominant natural diet of Calanus sinicus, a cold-temperate calanoid copepod that supports secondary production of important fisheries in the shelf ecosystems of the Northwest Pacific Ocean, Yellow Sea, Sea of Japan and South China Sea. In this study, the effect of the oxylipin-producing diatom Skeletonema marinoi on C. sinicus has been evaluated by analyzing expression level changes of genes involved in defense and detoxification systems. Results show that C. sinicus is more resistant to a diet of this diatom species in terms of gene expression patterns, compared to the congeneric species Calanus helgolandicus which is an important constituent of the temperate waters of the Atlantic Ocean and northern Mediterranean Sea. These findings contribute to the better understanding of genetic and/or phenotypic flexibility of copepod species and their capabilities to cope with stress by identifying molecular markers (such as stress and detoxification genes) as biosensors for environmental perturbations (e.g. toxins and contaminants) affecting marine copepods. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Phytoplankton food quality determines time windows for successful zooplankton reproductive pulses.

PubMed

Vargas, Cristian A; Escribano, Rubén; Poulet, Serge

2006-12-01

Recruitment success at the early life stages is a critical process for zooplankton demography. Copepods often dominate the zooplankton in marine coastal zones and are prey of the majority of fish larvae. Hypotheses interpreting variations of copepod recruitment are based on the concepts of "naupliar predation," "nutritional deficiency," and "toxic effect" of diatom diets. Contradictory laboratory and field studies have reached opposite conclusions on the effects of diatoms on copepod reproductive success, blurring our view of marine food-web energy flow from diatoms to higher consumers by means of copepods. Here we report estimates of copepod feeding selectivity and reproduction in response to seasonally changing phytoplankton characteristics measured in a highly productive coastal upwelling area off the coast of central Chile. The variable phytoplankton diversity and changing food quality had a strong and highly significant impact on the feeding selectivity, reproduction, and larval survival of three indigenous copepod species. Seasonal changes in copepod feeding behavior were related to the alternating protozoan-diatom diets, mostly based on dinoflagellates and ciliates during winter and autumn (low highly unsaturated fatty acids [HUFA]/polyunsaturated fatty acids [PUFA] availability), but switched to a diet of centric and chain-forming diatoms (high HUFA/PUFA availability) during the spring/summer upwelling period. Ingestion of diatom cells induced a positive effect on egg production. However, a negative relationship was found between egg hatching success, naupliar survival, and diatom ingestion. Depending on the phytoplankton species, diets had different effects on copepod reproduction and recruitment. In consequence, it seems that the classical marine food web model does not apply to some coastal upwelling systems.

What controls silicon isotope fractionation during dissolution of diatom opal?

NASA Astrophysics Data System (ADS)

Wetzel, F.; de Souza, G. F.; Reynolds, B. C.

2014-04-01

The silicon isotope composition of opal frustules from photosynthesising diatoms is a promising tool for studying past changes in the marine silicon cycle, and indirectly that of carbon. Dissolution of this opal may be accompanied by silicon isotope fractionation that could disturb the pristine silicon isotope composition of diatom opal acquired in the surface ocean. It has previously been shown that dissolution of fresh and sediment trap diatom opal in seawater does fractionate silicon isotopes. However, as the mechanism of silicon isotope fractionation remained elusive, it is uncertain whether opal dissolution in general is associated with silicon isotope fractionation considering that opal chemistry and surface properties are spatially and temporally (i.e. opal of different age) diverse. In this study we dissolved sediment core diatom opal in 5 mM NaOH and found that this process is not associated with significant silicon isotope fractionation. Since no variability of the isotope effect was observed over a wide range of dissolution rates, we can rule out the suggestion that back-reactions had a significant influence on the net isotope effect. Similarly, we did not observe an impact of temperature, specific surface area, or degree of undersaturation on silicon isotope partitioning during dissolution, such that these can most likely also be ruled out as controlling factors. We discuss the potential impacts of the chemical composition of the dissolution medium and age of diatom opal on silicon isotope fractionation during dissolution. It appears most likely that the controlling mechanism of silicon isotope fractionation during dissolution is related to the reactivity, or potentially, aluminium content of the opal. Such a dependency would imply that silicon isotope fractionation during dissolution of diatom opal is spatially and temporally variable. However, since the isotope effects during dissolution are small, the silicon isotope composition of diatom opal appears to be robust against dissolution in the deep sea sedimentary environment.

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.

PubMed

Smith, Sarah R; Gillard, Jeroen T F; Kustka, Adam B; McCrow, John P; Badger, Jonathan H; Zheng, Hong; New, Ashley M; Dupont, Chris L; Obata, Toshihiro; Fernie, Alisdair R; Allen, Andrew E

2016-12-01

Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success.

Cenozoic Planktonic Marine Diatom Diversity and Correlation to Climate Change

PubMed Central

Lazarus, David; Barron, John; Renaudie, Johan; Diver, Patrick; Türke, Andreas

2014-01-01

Marine planktonic diatoms export carbon to the deep ocean, playing a key role in the global carbon cycle. Although commonly thought to have diversified over the Cenozoic as global oceans cooled, only two conflicting quantitative reconstructions exist, both from the Neptune deep-sea microfossil occurrences database. Total diversity shows Cenozoic increase but is sample size biased; conventional subsampling shows little net change. We calculate diversity from a separately compiled new diatom species range catalog, and recalculate Neptune subsampled-in-bin diversity using new methods to correct for increasing Cenozoic geographic endemism and decreasing Cenozoic evenness. We find coherent, substantial Cenozoic diversification in both datasets. Many living cold water species, including species important for export productivity, originate only in the latest Miocene or younger. We make a first quantitative comparison of diatom diversity to the global Cenozoic benthic ∂18O (climate) and carbon cycle records (∂13C, and 20-0 Ma pCO2). Warmer climates are strongly correlated with lower diatom diversity (raw: rho = .92, p<.001; detrended, r = .6, p = .01). Diatoms were 20% less diverse in the early late Miocene, when temperatures and pCO2 were only moderately higher than today. Diversity is strongly correlated to both ∂13C and pCO2 over the last 15 my (for both: r>.9, detrended r>.6, all p<.001), but only weakly over the earlier Cenozoic, suggesting increasingly strong linkage of diatom and climate evolution in the Neogene. Our results suggest that many living marine planktonic diatom species may be at risk of extinction in future warm oceans, with an unknown but potentially substantial negative impact on the ocean biologic pump and oceanic carbon sequestration. We cannot however extrapolate our my-scale correlations with generic climate proxies to anthropogenic time-scales of warming without additional species-specific information on proximate ecologic controls. PMID:24465441

Drivers of Change in a 7300-Year Holocene Diatom Record from the Hemi-Boreal Region of Ontario, Canada

PubMed Central

Beck, Kristen K.; Medeiros, Andrew S.

2016-01-01

A Holocene lake sediment record spanning the past 7300 years from Wishart Lake in the Turkey Lakes Watershed in the Hemi-Boreal of central Ontario, Canada, was used to evaluate the potential drivers of long-term change in diatom assemblages at this site. An analysis of diatom assemblages found that benthic and epiphytic taxa dominated the mid-Holocene (7300–4000 cal yr BP), indicating shallow, oligotrophic, circum-neutral conditions, with macrophytes present. A significant shift in diatom assemblages towards more planktonic species (mainly Cyclotella sensu lato, but also several species of Aulacoseira, and Tabellaria flocculosa) occurred ~4000 cal yr BP. This change likely reflects an increase in lake level, coincident with the onset of a more strongly positive moisture balance following the drier climates of the middle Holocene, established by numerous regional paleoclimate records. Pollen-inferred regional changes in vegetation around 4000 yrs BP, including an increase in Betula and other mesic taxa, may have also promoted changes in diatom assemblages through watershed processes mediated by the chemistry of runoff. A more recent significant change in limnological conditions is marked by further increases in Cyclotella sensu lato beginning in the late 19th century, synchronous with the Ambrosia pollen rise and increases in sediment bulk density, signaling regional and local land clearance at the time of Euro-Canadian settlement (1880 AD). In contrast to the mid-Holocene increase in planktonic diatoms, the modern increase in Cyclotella sensu lato likely indicates a response to land use and vegetation change, and erosion from the watershed, rather than a further increase in water level. The results from Wishart Lake illustrate the close connection between paleoclimate change, regional vegetation, watershed processes, and diatom assemblages and also provides insight into the controls on abundance of Cyclotella sensu lato, a diatom taxonomic group which has shown significant increases and complex dynamics in the post-industrial era in lakes spanning temperate to Arctic regions. PMID:27532216

Seasonal trends in the pigment and amino acid compositions of sinking particles in biogenic CaCO 3 and SiO 2 dominated regions of the Pacific sector of the Southern Ocean along 170°W

NASA Astrophysics Data System (ADS)

Ingalls, Anitra E.; Liu, Zhanfei; Lee, Cindy

2006-05-01

We investigated amino acids and pigments in particles settling through the water column of the Southern Ocean and showed that spatial and temporal differences in phytoplankton source and consumer population influence sinking particle composition. Sediment traps were deployed along 170°W from November 1996 to March 1998 as part of the United States Joint Global Ocean Flux Study (US JGOFS) Antarctic Environment Southern Ocean Process Study (AESOPS) program. Peak fluxes of amino acids and pigments occurred during austral spring and summer (November-April) and were highest in the Antarctic Circumpolar Current (ACC). Compositional changes in pigments and total hydrolyzed amino acids demonstrate how the source of sinking particles varies with latitude and suggest that sinking material was most degraded in relatively diatom-depleted regions and toward the end of the high-flux period (February-March). At the Subantarctic Front, high proportions of pheophytin and β-alanine illustrate the important role of microbes in degradation. Further south at the Antarctic Polar Front, glycine, pyropheophorbide, and pheophorbide enrichments reflected a greater contribution of diatoms and greater processing by zooplankton grazers. Even further south in the ACC, enrichments of the diatom pigment fucoxanthin, diatom cell wall indicators glycine and serine, and diatom frustule-bound amino acids suggested the settling of empty frustules and aggregates. Despite being protected by the mineral, diatom-bound amino acids were not preferentially preserved between shallow and deep traps, possibly because of silica dissolution and a relatively small amount of organic carbon remineralization. Our results show that organic matter at diatom-rich stations is removed by mechanisms that do not result in the appearance of organic matter degradation indicators. Recent observations that calcium carbonate has a higher carrying capacity for sinking organic matter than silica may be related to diatom silicification, physiological status and decomposition pathway.

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

PubMed Central

McCrow, John P.; Badger, Jonathan H.; Zheng, Hong; New, Ashley M.; Dupont, Chris L.; Obata, Toshihiro; Fernie, Alisdair R.; Allen, Andrew E.

2016-01-01

Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success. PMID:27973599

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

DOE PAGES

Smith, Sarah R.; Gillard, Jeroen T. F.; Kustka, Adam B.; ...

2016-12-14

Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved inmore » the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success.« less

SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects

PubMed Central

2014-01-01

Background Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and/or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. Results The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Conclusions Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems. PMID:24964954

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Sarah R.; Gillard, Jeroen T. F.; Kustka, Adam B.

Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved inmore » the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success.« less

High-resolution paleoclimatology of the Santa Barbara Basin during the Medieval Climate Anomaly and early Little Ice Age based on diatom and silicoflagellate assemblages in Kasten core SPR0901-02KC

USGS Publications Warehouse

Barron, John A.; Bukry, David B.; Hendy, Ingrid L.

2015-01-01

Diatom and silicoflagellate assemblages documented in a high-resolution time series spanning 800 to 1600 AD in varved sediment recovered in Kasten core SPR0901-02KC (34°16.845’ N, 120°02.332’ W, water depth 588 m) from the Santa Barbara Basin (SBB) reveal that SBB surface water conditions during the Medieval Climate Anomaly (MCA) and the early part of the Little Ice Age (LIA) were not extreme by modern standards, mostly falling within one standard deviation of mean conditions during the pre anthropogenic interval of 1748 to 1900. No clear differences between the character of MCA and the early LIA conditions are apparent. During intervals of extreme droughts identified by terrigenous proxy scanning XRF analyses, diatom and silicoflagellate proxies for coastal upwelling typically exceed one standard deviation above mean values for 1748-1900, supporting the hypothesis that droughts in southern California are associated with cooler (or La Niña-like) sea surface temperatures (SSTs). Increased percentages of diatoms transported downslope generally coincide with intervals of increased siliciclastic flux to the SBB identified by scanning XRF analyses. Diatom assemblages suggest only two intervals of the MCA (at ~897 to 922 and ~1151 to 1167) when proxy SSTs exceeded one standard deviation above mean values for 1748 to 1900. Conversely, silicoflagellates imply extreme warm water events only at ~830 to 860 (early MCA) and ~1360 to 1370 (early LIA) that are not supported by the diatom data. Silicoflagellates appear to be more suitable for characterizing average climate during the 5 to 11 year-long sample intervals studied in the SPR0901-02KC core than diatoms, probably because diatom relative abundances may be dominated by seasonal blooms of a particular year.

Biochemical Composition of Dissolved Organic Matter Released During Experimental Diatom Blooms

NASA Technical Reports Server (NTRS)

Mannino, Antonio; Harvey, H. Rodger

2002-01-01

An axenic culture of Skeletonema costatum was grown to late-log phase to examine the molecular weight distribution and the biochemical composition of high molecular weight dissolved organic matter released in the absence of actively growing bacteria. A second culture was grown in a 5 m(exp 3) mesocosm and placed in darkness for a period of 51 days to examine the impact of phytoplankton bloom dynamics and microbial decomposition on dissolved (DOM) and particulate organic matter (POM) composition. DOM was separated using tangential-flow ultrafiltration into three nominal size fractions: LDOM (less than 1 kDa DOM), HDOM (1-30 kDa) and VHDOM (30 kDa-0.2 micron) and characterized. Both axenic and mesocosm diatom blooms released 28-33% of net primary production as dissolved organic carbon (DOC). In the axenic culture, HDOM and LDOM each comprised about half of the diatom-released DOC with less than l% as VHDOM. Diatoms from both experiments released carbohydrate-rich high molecular weight DOM. Much of the axenic diatom-released high molecular weight DOC could be chemically characterized (61% of HDOM and 78% of VHDOM) with carbohydrates as the primary component (45% of HDOM and 55% of VHDOM). Substantial amounts of hydrolyzable amino acids (16% of HDOM and 22% of VHDOM) and small amounts of lipids (less than 1%) were also released. Proportions of recognizable biochemical components in DOM produced in the mesocosm bloom were lower compared to the axenic culture. The presence of bacterial fatty acids and peptidoglycan-derived D-amino acids within high molecular weight fractions from the mesocosm bloom revealed that bacteria contributed a variety of macromolecules to DOM during the growth and decay of the diatom bloom. Release of significant amounts of DOC by diatoms demonstrates that DOM excretion is an important component of phytoplankton primary production. Similarities in high molecular weight DOM composition in marine waters and diatom cultures highlight the importance of phytoplankton to DOM composition in the ocean.

Dynamics of late spring and summer phytoplankton communities on Georges Bank, with emphasis on diatoms, Alexandrium spp., and other dinoflagellates

NASA Astrophysics Data System (ADS)

Gettings, Rachel M.; Townsend, David W.; Thomas, Maura A.; Karp-Boss, Lee

2014-05-01

We analyzed the distribution, abundance, and succession patterns of major phytoplankton taxa on Georges Bank in relation to hydrography, nutrients, and size-fractionated chlorophyll concentrations (>20 μm; <20 μm) on three oceanographic cruises from late spring through summer 2008 (28 April-5 May, 27 May-4 June, and 27 June-3 July). The April-May phytoplankton community was dominated numerically by the diatoms Skeletonema spp., Thalassiosira spp., Coscinodiscus spp., and Chaetoceros spp., with highest total diatom cell densities exceeding 200,000 cells l-1 on the Northeast Peak. In May-June, low nitrate and silicate concentrations over the Bank, along with patches of slightly elevated ammonium, were apparently supporting a predominantly dinoflagellate population; the toxic dinoflagellate Alexandrium spp. reached 13,000 cells l-1. Diatom cell densities on the second cruise in May-June were less than 60,000 cells l-1 and their spatial distributions did not overlap with the highest cell densities of Alexandrium spp. or other dinoflagellates. On the third and last cruise, in June-July, reduced nitrate and silicate concentrations were accompanied by a shift in the phytoplankton community: Alexandrium spp. cell densities were lower and heterotrophic and mixotrophic dinoflagellates, notably Polykrikos spp., Gyrodinium spp., Gymnodinium spp., and Prorocentrum spp., had become more abundant. Patches of regenerated silicate during the June-July period appeared to support a post-spring-bloom diatom community on the central crest of the Bank (total diatom cell densities >180,000 cellsl-1) of Leptocylindrus spp., Dactyliosolen spp., and Guinardia flaccida. Multivariate statistical analyses of phytoplankton taxa and station locations revealed distinct assemblages of diatom and dinoflagellate taxa on the Bank throughout the late spring and summer. Results are interpreted in the ecological context of earlier-reported laboratory culture experiments on the competitive interactions between Alexandrium fundyense and diatoms.

SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects.

PubMed

Kloster, Michael; Kauer, Gerhard; Beszteri, Bánk

2014-06-25

Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and/or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems.

Cenozoic planktonic marine diatom diversity and correlation to climate change.

PubMed

Lazarus, David; Barron, John; Renaudie, Johan; Diver, Patrick; Türke, Andreas

2014-01-01

Marine planktonic diatoms export carbon to the deep ocean, playing a key role in the global carbon cycle. Although commonly thought to have diversified over the Cenozoic as global oceans cooled, only two conflicting quantitative reconstructions exist, both from the Neptune deep-sea microfossil occurrences database. Total diversity shows Cenozoic increase but is sample size biased; conventional subsampling shows little net change. We calculate diversity from a separately compiled new diatom species range catalog, and recalculate Neptune subsampled-in-bin diversity using new methods to correct for increasing Cenozoic geographic endemism and decreasing Cenozoic evenness. We find coherent, substantial Cenozoic diversification in both datasets. Many living cold water species, including species important for export productivity, originate only in the latest Miocene or younger. We make a first quantitative comparison of diatom diversity to the global Cenozoic benthic ∂(18)O (climate) and carbon cycle records (∂(13)C, and 20-0 Ma pCO2). Warmer climates are strongly correlated with lower diatom diversity (raw: rho = .92, p<.001; detrended, r = .6, p = .01). Diatoms were 20% less diverse in the early late Miocene, when temperatures and pCO2 were only moderately higher than today. Diversity is strongly correlated to both ∂(13)C and pCO2 over the last 15 my (for both: r>.9, detrended r>.6, all p<.001), but only weakly over the earlier Cenozoic, suggesting increasingly strong linkage of diatom and climate evolution in the Neogene. Our results suggest that many living marine planktonic diatom species may be at risk of extinction in future warm oceans, with an unknown but potentially substantial negative impact on the ocean biologic pump and oceanic carbon sequestration. We cannot however extrapolate our my-scale correlations with generic climate proxies to anthropogenic time-scales of warming without additional species-specific information on proximate ecologic controls.

Using diatoms, hydrochemical and stable isotope tracers to infer runoff generation processes

NASA Astrophysics Data System (ADS)

Martínez-Carreras, N.; Wetzel, C. E.; Frentress, J.; Hlúbiková, D.; Ector, L.; McDonnell, J. J.; Hoffmann, L.; Pfister, L.

2012-04-01

Imaginative techniques are needed to improve our understanding of runoff generation processes. In this context, the hydrological community calls to cut across disciplines looking for new and exciting advances in knowledge. In this study, hydrologists and ecologists have worked together to use not only hydrochemical and stable isotope tracers, but also diatoms to infer runoff generation processes. Diatoms, one of the most common and divers algal group, can be easily transported by flowing water due to their small size (~10-200 μm). They are present in most terrestrial habitats and their diversified species distributions are largely controlled by physico-geographical factors (e.g. light, temperature, pH and moisture). Thus, hydrological systems largely control diatom species community composition and distribution. This study was conducted in the schistose Weierbach catchment (0.45 km2, NW Luxembourg). Its runoff regime is characterised by seasonal variation and a delayed shallow groundwater component originating from a saprolite zone. The catchment was instrumented with piezometers, suction cups, an automatic streamwater sampler, a sequential rainfall sampler, and soil moisture and temperature sensors. Samples collected bi-weekly and during storm runoff events allowed the characterisation of the different end-members. Chemical and isotopic hydrograph separations of stream discharge were used to determine not only the geographic sources of water, but also the fractions of old and new water contributing to streamflow. Diatoms intra-storm variability was also analysed and samples of diatoms from various terrestrial and subaerial substrates (bryophytes, litter and leaves), as well as from aquatic habitats (epilithon, epipelon and drift samples) were regularly collected. Diatoms were then used to constrain assumptions and to confirm or reject the hypothesis of existing surface runoff during rainfall-runoff events and to document the intermittent character of hydrological connectivity between upland, riparian and aquatic zones. As an advantage, diatoms do not seem to be subject to some inherent limitations of the classical tracer-based hydrograph separation techniques, such as unrealistic mixing assumptions, unstable end-member solutions and temporally varying input concentrations. Results suggested a substantial contribution of soil water during winter events in the Weierbach catchment, whereas groundwater played a more significant role during summer events. Even though overland flow remained insignificant during most of the sampled events, terrestrial diatom abundance increased with precipitation in all sampled events suggesting a rapid connectivity between soil surface and stream water. We hypothesise the mobilization and flushing away of terrestrial diatoms through a subsurface network of macropores in the shallow soils.

Response of the diatom flora in the Gdańsk Basin (southern Baltic Sea) to eutrophication in the last century

NASA Astrophysics Data System (ADS)

Witak, Małgorzata

2016-04-01

The diatom flora in six short cores (length of 10-20 cm) taken from Gdańsk Basin, southern Baltic Sea, was analyzed in order to response of diatoms to environmental changes over the past 100 years. This study is a part of CLISED project (Climate Change Impact on Ecosystem Health - Marine Sediments Indicators) funded from Norway Grants in the Polish-Norwegian Research Programme. Three cores P116, M1 and P1 were retrieved from the Gdańsk Deep region, whereas P104, BMPK10 and P110 were drilled from the shallower part - Gulf of Gdańsk. The sediment cores were dated by 210Pb and represented time interval of AD 1895-2015. In this period an artificial mouth of the Vistula River near Świbno was excavated and riverine waters flowed directly to the Gulf of Gdańsk. Urbanization, progressive industrialization and an increase in the inflow of waste water had a strong influence on ecosystem in the last 120 years. The transport of large amounts of nutrients, organic matter and pollutants by the rivers resulted in environmental degradation of the Gdańsk Basin and its progressive eutrophication in particular. Diatoms, being the major component of algal assemblages, are excellent bioindicators for assessing the state of basin ecosystems. They are usually abundant in marine sediments, diverse and sensitive to numerous environmental variables, including physical (e.g. light, temperature, water transparency) and chemical (e.g. pH, alkalinity, nutrient availability) factors. Changes in nutrients concentrations may lead to substantial transformations in the structure of diatom assemblages. Samples for diatom analyses (ca. 0.3-2.0 g dry sediment) were prepared following the standard procedure for diatom observation under light microscope (Battarbee, 1986). To estimate the concentration of siliceous microfossils per unit weight of dry sediment (absolute abundance), a random settling technique was used (Bodén, 1991). Permanent diatom preparations were mounted in Naphrax® (refractive index nD=1.73). The analysis was performed with a NIKON microscope under a 100× oil immersion objective. The raw counts were transformed to relative abundance of the total frustules counted. The diatoms were divided into groups according to their biotype, salinity, trophy and saproby requirements. The content (in percentage) of all ecological groups were counted in the core. A total of 145 diatom species including varieties and forms representing 53 genera were identified in all samples. The diatom community was strong dominance by small-size planktic euhalobous (Thalassiosira levanderi, Pauliella taeniata) and mesohalobous (Cyclotella choctawhatcheeana) species. They were accompanied by freshwater eutraphentic and pollution-tolerant forms Actinocyclus normanii, Cyclostephanos dubius, Cyclotella atomus, C. caspia, C. meneghiniana, Stephanodiscus hantzschii, S. medius, S. neoastraea and S. parvus. The assemblage structure is a visible evidence of the progressive anthropopressure recorded in the near-bottom sediments of the Gdańsk Basin. Moreover, changes in spatial distribution of diatom anthropogenic assemblage show the close relationship to the distance from mouth of the Vistula River.

A THz Tomography System for Arbitrarily Shaped Samples

NASA Astrophysics Data System (ADS)

Stübling, E.; Bauckhage, Y.; Jelli, E.; Fischer, B.; Globisch, B.; Schell, M.; Heinrich, A.; Balzer, J. C.; Koch, M.

2017-10-01

We combine a THz time-domain spectroscopy system with a robotic arm. With this scheme, the THz emitter and receiver can be positioned perpendicular and at defined distance to the sample surface. Our system allows the acquisition of reflection THz tomographic images of samples with an arbitrarily shaped surface.

Generation of arbitrarily shaped picosecond optical pulses using an integrated electrooptic waveguide modulator.

PubMed

Haner, M; Warren, W S

1987-09-01

We have produced complex software adjustable laser pulse shapes with ~10-ps resolution, and pulse energies up to 100 microJ for spectroscopic applications. The key devices are a high damage threshold electrooptic directional coupler and a GaAs circuit for synthesizing arbitrarily shaped microwave pulses.

Investigation of the Feasibility of Using Laser Induced Fluorescence for Concentration Measurements by Diatomic Sulfur.

DTIC Science & Technology

1982-12-01

GEP/PH/82D-1O INVESTIGATION OF THE FEASIBILITY OF USING LASER INDUCED FLUORESCENCE FOR CONCENTRATION MEASUREMENTS OF DIATOMIC SULFUR THESIS AFIT/GEP...FEASIBILITY OF USING LASER INDUCED FLUORESCENCE FOR CONCENTRATION MEASUREMENTS OF DIATOMIC SULFUR THESIS Presented to the Faculty of the School of...December 1982 SPecial Approved for public release; distribution unlimited Preface This thesis presented a rare opportunity and a formidable challenge

Resonant inelastic collisions of electrons with diatomic molecules

NASA Astrophysics Data System (ADS)

Houfek, Karel

2012-05-01

In this contribution we give a review of applications of the nonlocal resonance theory which has been successfully used for treating the nuclear dynamics of low-energy electron collisions with diatomic molecules over several decades. We give examples and brief explanations of various structures observed in the cross sections of vibrational excitation and dissociative electron attachment to diatomic molecules such as threshold peaks, boomerang oscillations below the dissociative attachment threshold, or outer-well resonances.

Paleogeographic evolution and paleoenvironmental reconstruction of the Sudd area during the Early-Mid Holocene, Sudan

NASA Astrophysics Data System (ADS)

El Shafie, Abdel Gadir A. I.; Elsayed Zeinelabdein, Khalid A.; Eisawi, Ali A. M.

2011-04-01

Sixty-five diatom species were identified from five localities within the top Umm Ruwaba Formation (namely Bara A, Bara B, Binaya, Sayal and Kosti). The recovered diatoms have been used here to confirm the existence of the so-called Lake Sudd, which once covered parts of central and southern Sudan, and lasted from 5.253 to 11.300 Ka B.P. The diatom assemblage indicates deposition in fresh to slightly saline water. The distribution of large-sized diatoms, noted within the study material, is attributed to the presence of spots characterized by high nutrition which correspond to the beach of the ancient lake. Integration of the paleontological results and remote sensing data permits the delineation of the lake boundary.

Diatoms: a fossil fuel of the future.

PubMed

Levitan, Orly; Dinamarca, Jorge; Hochman, Gal; Falkowski, Paul G

2014-03-01

Long-term global climate change, caused by burning petroleum and other fossil fuels, has motivated an urgent need to develop renewable, carbon-neutral, economically viable alternatives to displace petroleum using existing infrastructure. Algal feedstocks are promising candidate replacements as a 'drop-in' fuel. Here, we focus on a specific algal taxon, diatoms, to become the fossil fuel of the future. We summarize past attempts to obtain suitable diatom strains, propose future directions for their genetic manipulation, and offer biotechnological pathways to improve yield. We calculate that the yields obtained by using diatoms as a production platform are theoretically sufficient to satisfy the total oil consumption of the US, using between 3 and 5% of its land area. Copyright © 2014 Elsevier Ltd. All rights reserved.

Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

2018-04-01

We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

Diatom assemblage responses to changing environment in the conspicuously eutrophic Kiuruvesi lake route, central-eastern Finland

NASA Astrophysics Data System (ADS)

Tammelin, Mira; Kauppila, Tommi

2016-04-01

Lakes and their water quality have been affected by anthropogenic actions for centuries. The most intensive changes have often occurred since the mid-19th century. Industrialization, modern agriculture, forest ditching and artificial lowering of water level are examples of these changes that have usually resulted in the deterioration of lake water quality. Many organisms, such as diatoms, are sensitive to these changes in their environmental conditions. Therefore, a marked species turnover is often seen between the pre and post human impact diatom assemblages. This turnover can be rapidly assessed simultaneously from many lakes by using multivariate methods and top-bottom sampling. Our study area consists of three adjacent lake routes in the grass cultivation and dairy production area of central-eastern Finland, where slash-and-burn cultivation and artificial water level lowering were common practice during the past centuries. The centermost Iisalmi lake route is particularly interesting because of the conspicuously eutrophic lakes in its Kiuruvesi subroute. We used the top-bottom approach to sample pre and post human impact samples from 47 lakes (50 sampling sites) located in the three lake routes. In addition, stratigraphic samples from the long cores of three lakes (one larger central basin and two small upstream lakes) in the Kiuruvesi subroute were studied in more detail. Multivariate methods were used to assess diatom assemblage change within the long cores and between the pre-disturbance and modern samples. The results indicate that most study lakes have undergone a marked shift in their diatom assemblages since the onset of human impact in the area. The lake routes are characterized by differing pre-impact diatom assemblages. However, human influence has reduced their natural variation. Similar diatom species are common in the modern samples of the heavily impacted lakes in all three lake routes. The detailed examination of the diatom assemblage turnover in the three Kiuruvesi route lakes portrays different trajectories in each lake. The central basin has changed less than the upstream lakes. Two of the lakes have assemblage change trajectories that suggest increased nutrients, electrical conductivity, and pH. Unexpectedly, one of the upstream lakes shows an opposite trajectory, which might result from lowering water depth and improved living conditions for benthic diatoms.

From dipolar to multipolar interactions between ultracold Feshbach molecules

NASA Astrophysics Data System (ADS)

Quéméner, Goulven; Lepers, Maxence; Luc-Koenig, Eliane; Dulieu, Olivier

2016-05-01

Using the multipolar expansion of electrostatic and magnetostatic potential energies, we characterize the long-range interactions between two weakly-bound diatomic molecules, taking as an example the paramagnetic Er2 Feshbach molecules which were produced recently. The interaction between atomic magnetic dipoles gives rise to the usual R-3 leading term of the multipolar expansion, where R is the intermolecular distance. We show that additional terms scaling as R-5, R-7 and so on also appear, which are strongly anisotropic with respect to the orientation of the molecules. These terms can be seen as effective molecular multipole moments reflecting the spatial extension of the molecules which is non-negligible compared to R. We acknowledge the financial support of the COPOMOL project (ANR-13-IS04-0004) from Agence Nationale de la Recherche.

Diatoms as Proxies for a Fluctuating Ice Cap Margin, Hvitarvatn, Iceland

NASA Astrophysics Data System (ADS)

Black, J. L.; Miller, G. H.; Geirsdottir, A.

2005-12-01

There are no complete records of terrestrial environmental change for the Holocene (11,000yrs) in Iceland and the status of Icelandic glaciers in the early Holocene remains unclear. It is not even known whether Iceland's large ice caps disappeared in the early Holocene, and if they did, when they re-grew. Icelandic lakes are particularly well suited to address these uncertainties as: 1) Glacial erosion and soft bedrock result in high lacustrine sedimentation rates, 2) Diagnostic tephras aid the geochronology, 3) Iceland's sensitivity to changes in North Atlantic circulation should produce clear signals in key environmental proxies (diatoms) preserved in lacustrine sequences, and 4) Ice-cap profiles are relatively flat so small changes in the equilibrium line altitude result in large changes in accumulation area. Hence, large changes in ice-sheet margins during the Holocene will impact sedimentation in glacier-dominated lakes and the diatom assemblages at those times. Hvitarvatn is a glacier dominated lake located on the eastern margin of Langjokull Ice Cap in central-western Iceland. The uppermost Hvitarvatn sediments reflect a glacially dominated system with planktonic, silica-demanding diatom taxa that suggest a high dissolved silica and turbid water environment consistent with high fluxes of glacial flour. Below this are Neoglacial sediments deposited when Langjokull was active, but outlet glaciers were not in contact with Hvitarvatn. The diatom assemblage here shows a small increase in abundance, but is still dominated by planktic, silica-demanding taxa. A distinct shift in lake conditions is reflected in the lowermost sediments, composed of predominantly benthic diatoms and deposited in clear water conditions with long growing seasons likely found in an environment with warmer summers than present and with no glacial erosion. Langjokull must have disappeared in the early Holocene for such a diverse, benthic dominated diatom assemblage to flourish.

Biological responses of the marine diatom Chaetoceros socialis to changing environmental conditions: A laboratory experiment

PubMed Central

Roevros, Nathalie; Dehairs, Frank; Chou, Lei

2017-01-01

Diatoms constitute a major group of phytoplankton, accounting for ~20% of the world’s primary production. It has been shown that iron (Fe) can be the limiting factor for phytoplankton growth, in particular, in the HNLC (High Nutrient Low Chlorophyll) regions. Iron plays thus an essential role in governing the marine primary productivity and the efficiency of biological carbon pump. Oceanic systems are undergoing continuous modifications at varying rates and magnitudes as a result of changing climate. The objective of our research is to evaluate how changing environmental conditions (dust deposition, ocean warming and acidification) can affect marine Fe biogeochemistry and diatom growth. Laboratory culture experiments using a marine diatom Chaetoceros socialis were conducted at two temperatures (13°C and 18°C) and under two pCO2 (carbon dioxide partial pressure) (400 μatm and 800 μatm) conditions. The present study clearly highlights the effect of ocean acidification on enhancing the release of Fe upon dust deposition. Our results also confirm that being a potential source of Fe, dust provides in addition a readily utilizable source of macronutrients such as dissolved phosphate (PO4) and silicate (DSi). However, elevated atmospheric CO2 concentrations may also have an adverse impact on diatom growth, causing a decrease in cell size and possible further changes in phytoplankton composition. Meanwhile, ocean warming may lead to the reduction of diatom production and cell size, inducing poleward shifts in the biogeographic distribution of diatoms. The changing climate has thus a significant implication for ocean phytoplankton growth, cell size and primary productivity, phytoplankton distribution and community composition, and carbon (C), nitrogen (N), phosphorus (P), silicon (Si) and Fe biogeochemical cycles in various ways. PMID:29190826

Cenozoic planktonic marine diatom diversity and correlation to climate change

USGS Publications Warehouse

Lazarus, David; Barron, John; Renaudie, Johan; Diver, Patrick; Türke, Andreas

2014-01-01

Marine planktonic diatoms export carbon to the deep ocean, playing a key role in the global carbon cycle. Although commonly thought to have diversified over the Cenozoic as global oceans cooled, only two conflicting quantitative reconstructions exist, both from the Neptune deep-sea microfossil occurrences database. Total diversity shows Cenozoic increase but is sample size biased; conventional subsampling shows little net change. We calculate diversity from a separately compiled new diatom species range catalog, and recalculate Neptune subsampled-in-bin diversity using new methods to correct for increasing Cenozoic geographic endemism and decreasing Cenozoic evenness. We find coherent, substantial Cenozoic diversification in both datasets. Many living cold water species, including species important for export productivity, originate only in the latest Miocene or younger. We make a first quantitative comparison of diatom diversity to the global Cenozoic benthic ∂18O (climate) and carbon cycle records (∂13C, and 20-0 Ma pCO2). Warmer climates are strongly correlated with lower diatom diversity (raw: rho = .92, p2 were only moderately higher than today. Diversity is strongly correlated to both ∂13C and pCO2 over the last 15 my (for both: r>.9, detrended r>.6, all p<.001), but only weakly over the earlier Cenozoic, suggesting increasingly strong linkage of diatom and climate evolution in the Neogene. Our results suggest that many living marine planktonic diatom species may be at risk of extinction in future warm oceans, with an unknown but potentially substantial negative impact on the ocean biologic pump and oceanic carbon sequestration. We cannot however extrapolate our my-scale correlations with generic climate proxies to anthropogenic time-scales of warming without additional species-specific information on proximate ecologic controls.

Conserved Gene Order and Expanded Inverted Repeats Characterize Plastid Genomes of Thalassiosirales

PubMed Central

Ashworth, Matt P.; Baeshen, Nabih A.; Baeshen, Mohammad N.; Bahieldin, Ahmed; Theriot, Edward C.; Jansen, Robert K.

2014-01-01

Diatoms are mostly photosynthetic eukaryotes within the heterokont lineage. Variable plastid genome sizes and extensive genome rearrangements have been observed across the diatom phylogeny, but little is known about plastid genome evolution within order- or family-level clades. The Thalassiosirales is one of the more comprehensively studied orders in terms of both genetics and morphology. Seven complete diatom plastid genomes are reported here including four Thalassiosirales: Thalassiosira weissflogii, Roundia cardiophora, Cyclotella sp. WC03_2, Cyclotella sp. L04_2, and three additional non-Thalassiosirales species Chaetoceros simplex, Cerataulina daemon, and Rhizosolenia imbricata. The sizes of the seven genomes vary from 116,459 to 129,498 bp, and their genomes are compact and lack introns. The larger size of the plastid genomes of Thalassiosirales compared to other diatoms is due primarily to expansion of the inverted repeat. Gene content within Thalassiosirales is more conserved compared to other diatom lineages. Gene order within Thalassiosirales is highly conserved except for the extensive genome rearrangement in Thalassiosira oceanica. Cyclotella nana, Thalassiosira weissflogii and Roundia cardiophora share an identical gene order, which is inferred to be the ancestral order for the Thalassiosirales, differing from that of the other two Cyclotella species by a single inversion. The genes ilvB and ilvH are missing in all six diatom plastid genomes except for Cerataulina daemon, suggesting an independent gain of these genes in this species. The acpP1 gene is missing in all Thalassiosirales, suggesting that its loss may be a synapomorphy for the order and this gene may have been functionally transferred to the nucleus. Three genes involved in photosynthesis, psaE, psaI, psaM, are missing in Rhizosolenia imbricata, which represents the first documented instance of the loss of photosynthetic genes in diatom plastid genomes. PMID:25233465

The new diatom training set from the Polish Baltic coast and diatom-based transfer functions as a tool for understanding past changes in the southern Baltic coastal lakes

NASA Astrophysics Data System (ADS)

Lutyńska, Monika; Szpikowska, Grażyna; Woszczyk, Michał; Suchińska, Anita; Burchardt, Lubomira; Messyasz, Beata

2014-05-01

The transfer function method has been developed as a useful tool for reconstruction of the past environmental changes. It is based on the assumption that the modern species, which ecological requirements are known, can be used to quantitative reconstructions of the past changes. The aim of the study was to gather test sets and to build diatom-based transfer function, which can be used to reconstruct changes in the trophic state and salinity in the coastal lakes on the Polish Baltic coast. In the previous years there were several attempts made to reconstruct these parameters in lagoonal waters on the Baltic coasts in Germany, Denmark, Finland, Netherland, Sweden and Norway. But so far there is no diatom test set and transfer function was built for the Polish coastal lakes. We sample diatoms form 12 lakes located along the polish Baltic coast. At the same time we monitor the physical-chemical conditions in the lakes, which includes lake water chemical composition (chlorides, phosphorous and sulphur), pH, salinity, conductivity, temperature, dissolved oxygen. We collect samples form the lakes as well as from the Baltic Sea and we analyse the whole phytoplankton composition, however the special focus in put on diatoms. The results of the analysis show seasonal changes in the chemical and physical water properties. The diatom assemblage composition and species frequency also changed significantly. This study is a contribution to the projects: NN 306 064 640 financed by National Science Centre, Poland and Virtual Institute ICLEA (Integrated Climate and Landscape Evolution Analysis) funded by the Helmholtz Association.

Patterns of Genetic Diversity and Co-Existence in Open Ocean Diatoms: the Effects of Water Mass Structure, Selection and Sex

NASA Astrophysics Data System (ADS)

Rynearson, T. A.; Chen, G.

2016-02-01

The open ocean North Atlantic spring bloom influences regional ecology and global biogeochemistry. Diatoms dominate the peak of the bloom and significantly impact productivity and export of organic carbon from the bloom. Despite their key role in a yearly event with global impacts, the genetic diversity and population structure of diatoms that comprise this open ocean bloom are unknown. Here we investigated the population genetics of the diatom Thalassiosira gravida sampled during the 2008 North Atlantic Bloom Experiment using newly-developed microsatellite markers. Here, we show that the genetic diversity of open ocean diatoms is high and that their population structure differs dramatically from coastal diatoms. High levels of genetic diversity were observed across all water samples and did not change during the bloom. Four genetically distinct populations were identified but were not associated with different water masses, depths or time points during the bloom. Instead, all four populations co-existed within samples, spanning different water masses, stages of the bloom and depths of over >300 m. The pattern of genetically distinct, co-existing populations in the open ocean contrasts dramatically with coastal habitats, where distinct populations have not been observed to co-exist at the same time and place. It is likely that populations originate via transport from disparate locations combined with overwintering capacity in the water column or sediments. The pattern of co-existence suggests that the open ocean may serve as a gene pool that harbors different populations that are then available for selection to act upon, which may contribute to the ecological and biogeochemical success of diatoms and influence their long-term evolutionary survival.

Diatom assemblages from a turbid coastal plain estuary: Río de la Plata (South America)

NASA Astrophysics Data System (ADS)

Licursi, Magdalena; Sierra, María Victoria; Gómez, Nora

2006-08-01

The Río de la Plata is located on the East coast of South America and is a shallow, large-scale, turbid coastal plain estuary that covers an approximate area of 35,000 km 2. Despite the socio-economic importance of the Río de la Plata, studies related to the biological aspects of this ecosystem are scarce, particularly in the freshwater tidal zone. The objective of this study was to explore the diatom composition and distribution of density, biomass and empty frustules along the fluvial-mixohaline axis. Furthermore it was to analyze the spatial succession of diatom assemblages and the environmental variables during an extensive sampling carried out during spring 2001. Two replicate sub-surface water samples were collected at 29 sites for quantitative analysis of phytoplankton. The greatest number of species, mainly pennate taxa, were observed in the freshwater tidal zone. The average density of the diatoms was 59 cells ml - 1 . Chains or filaments of centric diatoms were frequent and dominant in the samples along the fluvial-mixohaline axis. The carbon content of the diatoms increased downstream, with an average value of 2.5 μg C l - 1 in the freshwater tidal zone and 4.4 μg C l - 1 in the mixohaline zone. Diatoms supplied 65% of the total phytoplankton carbon content in the freshwater tidal zone and reached 17% in the mixohaline zone. Canonical Correspondence Analysis (CCA) allowed us to identify two species assemblages in the Río de la Plata differentiated mainly by salinity, pH and silicate gradients. In our study species exclusive to brackish waters were not identified, but some freshwater and marine taxa with wide ranges of salinity tolerance were observed.

Determining diatom ecotones and their relationship to terrestrial ecoregion designations in the central Canadian Arctic Islands.

PubMed

Antoniades, Dermot; Douglas, Marianne S V; Michelutti, Neal; Smol, John P

2014-08-01

Ecotones are key areas for the detection of global change because many are predicted to move with shifts in climate. Prince of Wales Island, in the Canadian Arctic Archipelago, spans the transition between mid- to high-Arctic ecoregions. We analyzed limnological variables and recent diatom assemblages from its lakes and ponds to determine if assemblages reflected this ecotone. Limnological gradients were short, and water chemistry explained 20.0% of diatom variance in a redundancy analysis (RDA), driven primarily by dissolved organic carbon, Ca and SO4 . Most taxa were small, benthic forms; key taxa such as planktonic Cyclotella species were restricted to the warmer, southern portion of the study area, while benthic Staurosirella were associated with larger, ice-dominated lakes. Nonetheless, there were no significant changes in diatom assemblages across the mid- to high-Arctic ecoregion boundary. We combined our data set with one from nearby Cornwallis Island to expand the study area and lengthen its environmental gradients. Within this expanded data set, 40.6% of the diatom variance was explained by a combination of water chemistry and geographic variables, and significant relationships were revealed between diatom distributions and key limnological variables, including pH, specific conductivity, and chl-a. Using principal coordinates analysis, we estimated community turnover with latitude and applied piecewise linear regression to determine diatom ecotone positions. A pronounced transition was present between Prince of Wales Island and the colder, more northerly Cornwallis Island. These data will be important in detecting any future northward ecotone movement in response to predicted Arctic climate warming in this highly sensitive region. © 2014 Phycological Society of America.

Occurrence of Diatoms in Lakeside Wells in Northern New Jersey as an Indicator of the Effect of Surface Water on Ground-Water Quality

USGS Publications Warehouse

Reilly, Timothy J.; Walker, Christopher E.; Baehr, Arthur L.; Schrock, Robin M.; Reinfelder, John R.

2006-01-01

In a novel approach for detecting ground-water/surface-water interaction, diatoms were used as an indicator that surface water affects ground-water quality in lakeside communities in northern New Jersey. The presence of diatoms, which are abundant in lakes, in adjacent domestic wells demonstrated that ground water in these lakeside communities was under the direct influence of surface water. Entire diatom frustules were present in 17 of 18 water samples collected in August 1999 from domestic wells in communities surrounding Cranberry Lake and Lake Lackawanna. Diatoms in water from the wells were of the same genus as those found in the lakes. The presence of diatoms in the wells, together with the fact that most static and stressed water levels in wells were below the elevation of the lake surfaces, indicates that ground-water/surface-water interaction is likely. Ground-water/surface-water interaction also probably accounts for the previously documented near-ubiquitous presence of methyl tertiary-butyl ether in the ground-water samples. Recreational use of lakes for motor boating and swimming, the application of herbicides for aquatic weed control, runoff from septic systems and roadways, and the presence of waterfowl all introduce contaminants to the lake. Samples from 4 of the 18 wells contained Navicula spp., a documented significant predictor of Giardia and Cryptosporidium. Because private well owners in New Jersey generally are not required to regularly monitor their wells, and tests conducted by public-water suppliers may not be sensitive to indicators of ground-water/surface-water interaction, these contaminants may remain undetected. The presence of diatoms in wells in similar settings can warn of lake/well interactions in the absence of other indicators.

Spatial coherence of oriented white matter microstructure: Applications to white matter regions associated with genetic similarity.

PubMed

Hallgrímsson, Haraldur T; Cieslak, Matthew; Foschini, Luca; Grafton, Scott T; Singh, Ambuj K

2018-05-15

We present a method to discover differences between populations with respect to the spatial coherence of their oriented white matter microstructure in arbitrarily shaped white matter regions. This method is applied to diffusion MRI scans of a subset of the Human Connectome Project dataset: 57 pairs of monozygotic and 52 pairs of dizygotic twins. After controlling for morphological similarity between twins, we identify 3.7% of all white matter as being associated with genetic similarity (35.1 k voxels, p<10 -4 , false discovery rate 1.5%), 75% of which spatially clusters into twenty-two contiguous white matter regions. Furthermore, we show that the orientation similarity within these regions generalizes to a subset of 47 pairs of non-twin siblings, and show that these siblings are on average as similar as dizygotic twins. The regions are located in deep white matter including the superior longitudinal fasciculus, the optic radiations, the middle cerebellar peduncle, the corticospinal tract, and within the anterior temporal lobe, as well as the cerebellum, brain stem, and amygdalae. These results extend previous work using undirected fractional anisotrophy for measuring putative heritable influences in white matter. Our multidirectional extension better accounts for crossing fiber connections within voxels. This bottom up approach has at its basis a novel measurement of coherence within neighboring voxel dyads between subjects, and avoids some of the fundamental ambiguities encountered with tractographic approaches to white matter analysis that estimate global connectivity. Copyright © 2018 Elsevier Inc. All rights reserved.

Computer program to simulate Raman scattering

NASA Technical Reports Server (NTRS)

Zilles, B.; Carter, R.

1977-01-01

A computer program is described for simulating the vibration-rotation and pure rotational spectrum of a combustion system consisting of various diatomic molecules and CO2 as a function of temperature and number density. Two kinds of spectra are generated: a pure rotational spectrum for any mixture of diatomic and linear triatomic molecules, and a vibrational spectrum for diatomic molecules. The program is designed to accept independent rotational and vibrational temperatures for each molecule, as well as number densities.

Transport and distribution of bacteria and diatoms in the aqueous surface micro-layer of a salt marsh

USGS Publications Warehouse

Harvey, Ronald W.; Lion, Leonard W.; Young, Lily Y.

1983-01-01

The effects of tide and wind upon the distribution and transport of bacteria and diatoms in the aqueous surface microlayers of a Massachusetts and San Francisco Bay salt marsh were examined. The compression of the surface films by both tide and wind resulted in significant enrichments of bacterioneuston. At the San Francisco Bay site, significant numbers of diatoms were transported within the microlayer over a tidal cycle.

Photo-Oxidative Stress-Driven Mutagenesis and Adaptive Evolution on the Marine Diatom Phaeodactylum tricornutum for Enhanced Carotenoid Accumulation.

PubMed

Yi, Zhiqian; Xu, Maonian; Magnusdottir, Manuela; Zhang, Yuetuan; Brynjolfsson, Sigurdur; Fu, Weiqi

2015-09-29

Marine diatoms have recently gained much attention as they are expected to be a promising resource for sustainable production of bioactive compounds such as carotenoids and biofuels as a future clean energy solution. To develop photosynthetic cell factories, it is important to improve diatoms for value-added products. In this study, we utilized UVC radiation to induce mutations in the marine diatom Phaeodactylum tricornutum and screened strains with enhanced accumulation of neutral lipids and carotenoids. Adaptive laboratory evolution (ALE) was also used in parallel to develop altered phenotypic and biological functions in P. tricornutum and it was reported for the first time that ALE was successfully applied on diatoms for the enhancement of growth performance and productivity of value-added carotenoids to date. Liquid chromatography-mass spectrometry (LC-MS) was utilized to study the composition of major pigments in the wild type P. tricornutum, UV mutants and ALE strains. UVC radiated strains exhibited higher accumulation of fucoxanthin as well as neutral lipids compared to their wild type counterpart. In addition to UV mutagenesis, P. tricornutum strains developed by ALE also yielded enhanced biomass production and fucoxanthin accumulation under combined red and blue light. In short, both UV mutagenesis and ALE appeared as an effective approach to developing desired phenotypes in the marine diatoms via electromagnetic radiation-induced oxidative stress.

Photo-Oxidative Stress-Driven Mutagenesis and Adaptive Evolution on the Marine Diatom Phaeodactylum tricornutum for Enhanced Carotenoid Accumulation

PubMed Central

Yi, Zhiqian; Xu, Maonian; Magnusdottir, Manuela; Zhang, Yuetuan; Brynjolfsson, Sigurdur; Fu, Weiqi

2015-01-01

Marine diatoms have recently gained much attention as they are expected to be a promising resource for sustainable production of bioactive compounds such as carotenoids and biofuels as a future clean energy solution. To develop photosynthetic cell factories, it is important to improve diatoms for value-added products. In this study, we utilized UVC radiation to induce mutations in the marine diatom Phaeodactylum tricornutum and screened strains with enhanced accumulation of neutral lipids and carotenoids. Adaptive laboratory evolution (ALE) was also used in parallel to develop altered phenotypic and biological functions in P. tricornutum and it was reported for the first time that ALE was successfully applied on diatoms for the enhancement of growth performance and productivity of value-added carotenoids to date. Liquid chromatography-mass spectrometry (LC-MS) was utilized to study the composition of major pigments in the wild type P. tricornutum, UV mutants and ALE strains. UVC radiated strains exhibited higher accumulation of fucoxanthin as well as neutral lipids compared to their wild type counterpart. In addition to UV mutagenesis, P. tricornutum strains developed by ALE also yielded enhanced biomass production and fucoxanthin accumulation under combined red and blue light. In short, both UV mutagenesis and ALE appeared as an effective approach to developing desired phenotypes in the marine diatoms via electromagnetic radiation-induced oxidative stress. PMID:26426027

Seasonal distribution of Gambierdiscus spp. in Wakasa Bay, the Sea of Japan, and antagonistic relationships with epiphytic pennate diatoms.

PubMed

Nakada, Mitsutaka; Hatayama, Yuki; Ishikawa, Akira; Ajisaka, Tetsuro; Sawayama, Shigeki; Imai, Ichiro

2018-06-01

The occurrence of the ciguatera fish poisoning (CFP) causative Gambierdiscus spp. was confirmed in the Sea of Japan for the first time in 2009. This paper reports seasonal distribution of Gambierdiscus spp. and epiphytic diatoms in the Sea of Japan. Monitoring results suggested an antagonistic interaction in abundances between epiphytic diatoms and the dinoflagellate Gambierdiscus spp. Allelopathic effects of diatoms were considered to be involved in the competitive phenomenon. Therefore it is hypothesized that cell densities of epiphytic pennate diatoms on macroalgae are a novel determinant affecting the abundance of Gambierdiscus spp. other than sea water temperature, salinity and nutrients. Monitorings of the abundance of epiphytic diatoms would lead us to predict the occurrences of Gambierdiscus spp. blooms in the CFP area, and thereby the CFP risk assessments would be developed. Phylogenetic analyses indicated that Gambierdiscus spp. in the Sea of Japan belonged to Gambierdiscus sp. type 2 which was reported to be non-toxic. Nevertheless, based on morphological characteristics, at least two types of Gambierdiscus spp. were found in the Sea of Japan. It is needed to test the toxicity of the both types of Gambierdiscus recognized in the present study for evaluation of the probability of CFP outbreak risks in the Sea of Japan in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

Differential dissolution of Lake Baikal diatoms: correction factors and implications for palaeoclimatic reconstruction

NASA Astrophysics Data System (ADS)

Battarbee, Richard W.; Mackay, A. W.; Jewson, D. H.; Ryves, D. B.; Sturm, M.

2005-04-01

In order to assess how faithfully the composition of diatom assemblages in the recent sediments of Lake Baikal represents the composition of the planktonic diatom populations in the lake, we have compared the flux of diatoms from the water column (i.e., "expected" in the sediment) with the accumulation rates of the same diatom taxa (i.e., "observed" in the sediment) from BAIK 38, a sediment core collected in the south basin of the lake. Whilst there are many uncertainties, the results indicate that only approximately 1% of the phytoplankton crop is preserved in the sediment and some species are more affected by dissolution than others. These findings are comparable to similar studies undertaken in the marine environment. In terms of differential dissolution, our studies suggest that the endemic taxa (e.g., Cyclotella minuta and Aulacoseira baicalensis) are the most resilient, whereas cosmopolitan taxa such as Nitzschia acicularis and Synedra acus are the least resilient. N. acicularis dissolves in the water column, but for other taxa, most dissolution takes place at the surface sediment-water interface. We use the data to develop a series of species-specific correction factors that allow the composition of the source populations to be reconstituted, and we argue that failure to take these processes into account can undermine the use of the diatom and biogenic silica record in Lake Baikal for palaeo-productivity and palaeoclimate reconstruction.

How benthic diatoms within natural communities respond to eight common herbicides with different modes of action.

PubMed

Wood, Rebecca J; Mitrovic, Simon M; Lim, Richard P; Kefford, Ben J

2016-07-01

Herbicides are common pollutants of rivers in agricultural regions. These contaminants include various types of chemicals with different modes of toxic action. Herbicides can have toxic effects on freshwater benthic diatoms, the base of the aquatic food web. We examined the effects of (non-mixture) herbicide exposure to the health of diatoms for eight common herbicides with three different modes of action; the photosystem II (PSII) inhibitors: atrazine, simazine, hexazinone, tebuthiuron and diuron; two auxinic herbicides: MCPA and 2,4-D; and the EPSP synthase inhibitor: glyphosate. Benthic diatoms within riverine communities were exposed to each herbicide in rapid toxicity tests at concentrations of 50, 200 and 500μgL(-1). The most sensitive taxa were Gomphonema spp. and Encyonema gracilis. Navicula cryptotenella was the most tolerant to herbicide exposure. There was no significant effect of the different herbicide modes of action at the community level. Herbicide mode of action did not alter which taxa were most sensitive within the community and sensitivity rankings of the dominant diatom taxa were similar for each of the eight herbicides. The consistency of the results between herbicides suggests that freshwater benthic diatoms may be suitable in situ indicators for detecting the toxicity of herbicides with differing modes of action. Copyright © 2016 Elsevier B.V. All rights reserved.

Diatom assemblages as guides to flow conditions during the 2004 Indian Ocean tsunami at Phra Thong Island, Thailand

NASA Astrophysics Data System (ADS)

Sawai, Y.; Jankaew, K.; Martin, M. E.; Choowong, M.; Charoentitirat, T.; Prendergast, A.

2008-12-01

Diatom assemblages in the 2004 tsunami deposits of Phra Thong Island, Thailand represent flow conditions during the tsunami. The tsunami deposit consists of single or multiple graded beds. Diatom assemblages in the lowermost part of the deposit predominantly comprise beach and subtidal species. In the middle part of the deposit, the assemblages are dominated by marine plankton with increasing finer fractions. A mixed assemblage of freshwater, brackish, and marine species occupies the uppermost part of the deposit. Changes in flow conditions during the tsunami can explain these diatom assemblage variations. During fast current velocities, medium sand is deposited; only beach and subtidal diatoms that live attached to the sand can be incorporated into the tsunami deposit under these flow conditions. It is difficult for diatoms in suspension to settle out under fast current velocities. With decreasing current velocities, marine plankton can settle out of the water column .Finally, during the suspension stage (calm currents) between tsunami waves, the entrained freshwater, brackish, and marine species settle out with mud and plant trash. Fewer broken valves in the lowermost part of the deposit is probably a results of rapid entrainment, whilst selective breakage of marine plankton (Thalassionema nitzschioides, and Thalassiosira and Coscinodiscus spp.) in the middle part of the deposit probably results from abrasion by turbulent current before their deposition.

Growth and Proteome Response of Temperate and Polar Diatoms Thalassiosira pseudonana and Chaetoceros sp. to variations in Cobalt and Zinc: Identification of the High-Affinity Zinc Transporter and Potential for Use as a Biomarker

NASA Astrophysics Data System (ADS)

Kellogg, M. M.; Moran, D. M.; McIlvin, M. R.; Allen, A. E.; Saito, M. A.

2016-02-01

Marine diatoms such as the temperate Thalassiosira pseudonana (Tp) and the polar Chaetoceros sp (Ch) are known to be important contributors to marine primary productivity and the global carbon cycle. The nutritional use of zinc (Zn) in diatoms and the ability to substitute cobalt (Co) for Zn has been previously demonstrated to be of importance in their growth and biochemistry. We conducted physiological experiments with Zn and Co on these diatoms and analyzed their proteomic response. Growth studies involving Tp confirmed previous studies' findings showing Zn/Co substitution, while studies on Ch showed a toxic response to high Zn abundances. Proteome responses of Tp to Zn limitation identified a putative and previously unidentified transporter that was undetectable at high Zn concentration and became highly abundant at two lower Zn concentrations. The distribution of this protein in nature and its potential use as a Zn stress biomarker in diatoms will be discussed.

Continental erosion and the Cenozoic rise of marine diatoms

NASA Astrophysics Data System (ADS)

Cermeño, Pedro; Falkowski, Paul G.; Romero, Oscar E.; Schaller, Morgan F.; Vallina, Sergio M.

2015-04-01

Marine diatoms are silica-precipitating microalgae that account for over half of organic carbon burial in marine sediments and thus they play a key role in the global carbon cycle. Their evolutionary expansion during the Cenozoic era (66 Ma to present) has been associated with a superior competitive ability for silicic acid relative to other siliceous plankton such as radiolarians, which evolved by reducing the weight of their silica test. Here we use a mathematical model in which diatoms and radiolarians compete for silicic acid to show that the observed reduction in the weight of radiolarian tests is insufficient to explain the rise of diatoms. Using the lithium isotope record of seawater as a proxy of silicate rock weathering and erosion, we calculate changes in the input flux of silicic acid to the oceans. Our results indicate that the long-term massive erosion of continental silicates was critical to the subsequent success of diatoms in marine ecosystems over the last 40 My and suggest an increase in the strength and efficiency of the oceanic biological pump over this period.

Gyroscopic effect in low-energy classical capture of a rotating quadrupolar diatom by an ion.

PubMed

Dashevskaya, Elena; Litvin, Iliya; Nikitin, Evgueni

2006-03-09

The low-energy capture of homonuclear diatoms by ions is due mainly to the long-range part of the interpartner potential with leading terms that correspond to charge-quadrupole interaction and charge-induced dipole interaction. The capture dynamics is described by the perturbed-rotor adiabatic potentials and the Coriolis interaction between manifold of states that belong to a given value of the intrinsic angular momentum. When the latter is large enough, it can noticeably affect the capture cross section calculated in the adiabatic channel approximation due to the gyroscopic property of a rotating diatom. This paper presents the low-energy (low-temperature) state-selected partial and mean capture cross sections (rate coefficients) for the charge-quadrupole interaction that include the gyroscopic effect (decoupling of intrinsic angular momentum from the collision axis), quantum correction for the diatom rotation, and the correction for the charge-induced dipole interaction. These results complement recent studies on the gyroscopic effect in the quantum regime of diatom-ion capture (Dashevskaya, E. I.; Litvin, I.; Nikitin, E. E.; Troe, J. J. Chem. Phys. 2004, 120, 9989-9997).

Survival of fossils under extreme shocks induced by hypervelocity impacts.

PubMed

Burchell, M J; McDermott, K H; Price, M C; Yolland, L J

2014-08-28

Experimental data are shown for survival of fossilized diatoms undergoing shocks in the GPa range. The results were obtained from hypervelocity impact experiments which fired fossilized diatoms frozen in ice into water targets. After the shots, the material recovered from the target water was inspected for diatom fossils. Nine shots were carried out, at speeds from 0.388 to 5.34 km s(-1), corresponding to mean peak pressures of 0.2-19 GPa. In all cases, fragmented fossilized diatoms were recovered, but both the mean and the maximum fragment size decreased with increasing impact speed and hence peak pressure. Examples of intact diatoms were found after the impacts, even in some of the higher speed shots, but their frequency and size decreased significantly at the higher speeds. This is the first demonstration that fossils can survive and be transferred from projectile to target in hypervelocity impacts, implying that it is possible that, as suggested by other authors, terrestrial rocks ejected from the Earth by giant impacts from space, and which then strike the Moon, may successfully transfer terrestrial fossils to the Moon.

Survival of fossils under extreme shocks induced by hypervelocity impacts

PubMed Central

Burchell, M. J.; McDermott, K. H.; Price, M. C.; Yolland, L. J.

2014-01-01

Experimental data are shown for survival of fossilized diatoms undergoing shocks in the GPa range. The results were obtained from hypervelocity impact experiments which fired fossilized diatoms frozen in ice into water targets. After the shots, the material recovered from the target water was inspected for diatom fossils. Nine shots were carried out, at speeds from 0.388 to 5.34 km s−1, corresponding to mean peak pressures of 0.2–19 GPa. In all cases, fragmented fossilized diatoms were recovered, but both the mean and the maximum fragment size decreased with increasing impact speed and hence peak pressure. Examples of intact diatoms were found after the impacts, even in some of the higher speed shots, but their frequency and size decreased significantly at the higher speeds. This is the first demonstration that fossils can survive and be transferred from projectile to target in hypervelocity impacts, implying that it is possible that, as suggested by other authors, terrestrial rocks ejected from the Earth by giant impacts from space, and which then strike the Moon, may successfully transfer terrestrial fossils to the Moon. PMID:25071234

Continental erosion and the Cenozoic rise of marine diatoms

PubMed Central

Cermeño, Pedro; Falkowski, Paul G.; Romero, Oscar E.; Schaller, Morgan F.; Vallina, Sergio M.

2015-01-01

Marine diatoms are silica-precipitating microalgae that account for over half of organic carbon burial in marine sediments and thus they play a key role in the global carbon cycle. Their evolutionary expansion during the Cenozoic era (66 Ma to present) has been associated with a superior competitive ability for silicic acid relative to other siliceous plankton such as radiolarians, which evolved by reducing the weight of their silica test. Here we use a mathematical model in which diatoms and radiolarians compete for silicic acid to show that the observed reduction in the weight of radiolarian tests is insufficient to explain the rise of diatoms. Using the lithium isotope record of seawater as a proxy of silicate rock weathering and erosion, we calculate changes in the input flux of silicic acid to the oceans. Our results indicate that the long-term massive erosion of continental silicates was critical to the subsequent success of diatoms in marine ecosystems over the last 40 My and suggest an increase in the strength and efficiency of the oceanic biological pump over this period. PMID:25831504

Continental erosion and the Cenozoic rise of marine diatoms.

PubMed

Cermeño, Pedro; Falkowski, Paul G; Romero, Oscar E; Schaller, Morgan F; Vallina, Sergio M

2015-04-07

Marine diatoms are silica-precipitating microalgae that account for over half of organic carbon burial in marine sediments and thus they play a key role in the global carbon cycle. Their evolutionary expansion during the Cenozoic era (66 Ma to present) has been associated with a superior competitive ability for silicic acid relative to other siliceous plankton such as radiolarians, which evolved by reducing the weight of their silica test. Here we use a mathematical model in which diatoms and radiolarians compete for silicic acid to show that the observed reduction in the weight of radiolarian tests is insufficient to explain the rise of diatoms. Using the lithium isotope record of seawater as a proxy of silicate rock weathering and erosion, we calculate changes in the input flux of silicic acid to the oceans. Our results indicate that the long-term massive erosion of continental silicates was critical to the subsequent success of diatoms in marine ecosystems over the last 40 My and suggest an increase in the strength and efficiency of the oceanic biological pump over this period.

Salinity-dependent diatom biosilicification implies an important role of external ionic strength

PubMed Central

Vrieling, Engel G.; Sun, Qianyao; Tian, Mingwen; Kooyman, Patricia J.; Gieskes, Winfried W. C.; van Santen, Rutger A.; Sommerdijk, Nico A. J. M.

2007-01-01

The role of external ionic strength in diatom biosilica formation was assessed by monitoring the nanostructural changes in the biosilica of the two marine diatom species Thalassiosira punctigera and Thalassiosira weissflogii that was obtained from cultures grown at two distinct salinities. Using physicochemical methods, we found that at lower salinity the specific surface area, the fractal dimensions, and the size of mesopores present in the biosilica decreased. Diatom biosilica appears to be denser at the lower salinity that was applied. This phenomenon can be explained by assuming aggregation of smaller coalescing silica particles inside the silica deposition vesicle, which would be in line with principles in silica chemistry. Apparently, external ionic strength has an important effect on diatom biosilica formation, making it tempting to propose that uptake of silicic acid and other external ions may take place simultaneously. Uptake and transport of reactants in the proximity of the expanding silica deposition vesicle, by (macro)pinocytosis, are more likely than intracellular stabilization and transport of silica precursors at the high concentrations that are necessary for the formation of the siliceous frustule components. PMID:17563373

Effects of abiotic factors on the nanostructure of diatom frustules-ranges and variability.

PubMed

Su, Yanyan; Lundholm, Nina; Ellegaard, Marianne

2018-05-26

The intricate patterning of diatom silica frustules at nanometer-to-micrometer scales makes them of interest for a wide range of industrial applications. For some of these applications, a specific size range in nanostructure is required and may be achieved by selecting species with the desired properties. However, as all biological materials, diatom frustules exhibit variability in their morphological parameters and this variability can to some extent be affected and controlled by environmental conditions. In this review, we explore the effects of different environmental factors including salinity, heavy metals, temperature, pH, extracellular Si(OH) 4 or Ge(OH) 4 concentration, light regime, UV irradiance, long-term cultivation, and biotic factors on the nanostructure of diatom frustules. This compilation of studies illustrates that it is possible to affect the nanostructure of diatom frustules in vivo by controlling different environmental factors as well as by direct chemical modification of frustules. We compare these methods and present examples of how these changes affect the range of variability as well as comparing the magnitude of size changes of the most promising methods.

Community- and population-level changes in diatom size structure in a subarctic lake over the last two centuries

PubMed Central

Kerrigan, Elizabeth A.; Irwin, Andrew J.

2015-01-01

Climate change over the last two centuries has been associated with significant shifts in diatom community structure in lakes from the high arctic to temperate latitudes. To test the hypotheses that recent climate warming selects for species of smaller size within communities and a decrease in the average size of species within populations, we quantified the size of individual diatom valves from 10 depths in a sediment core covering the last ∼200 years from a pristine subarctic lake. Over the last ∼200 years, changes in the relative abundance of species of different average size and changes in the average valve size of populations of species contribute equally to the changes in community size structure, but are often opposite in sign, compensating for one another and moderating temporal changes in community size structure. In the surface sediments that correspond to the recent decades when air temperatures have warmed, the mean size of valves in the diatom community has significantly decreased due to an increase in the proportion of smaller-sized planktonic diatom species. PMID:26157637

Purification and culture characteristics of 36 benthic marine diatoms isolated from the Solthörn tidal flat (Southern North Sea).

PubMed

Scholz, Bettina

2014-08-01

Marine benthic diatoms growing in biofilms on sediment surfaces generally occur associated with heterotrophic bacteria, whereas modern molecular techniques and analyses of species-specific physiology create a demand for axenic cultures. Numerous benthic diatoms were isolated from surface sediments during a monitoring of the Solthörn tidal flat (southern North Sea, Germany) from May 2008 to May 2009. Of these, around 50% could be purified from the accompanying heterotrophic bacteria using different antibiotics combined with physical separation methods (vortexing, ultrasound). Overall, seven different antibiotics were tested at different concentrations, and a best working protocol was developed. The axenic strains were stable on average for only around 15 months, indicating a symbiotic interaction between the benthic diatoms and the associated bacteria. While most short-term effects during the purification process were restricted to differences in growth rates among xenic and axenic diatom strains, long-term cultivation led to distinct changes in cell volumes and growth characteristics of the axenic strains. © 2014 Phycological Society of America.

Chemical and Biological Sensing Using Diatom Photonic Crystal Biosilica With In-Situ Growth Plasmonic Nanoparticles.

PubMed

Kong, Xianming; Squire, Kenny; Li, Erwen; LeDuff, Paul; Rorrer, Gregory L; Tang, Suning; Chen, Bin; McKay, Christopher P; Navarro-Gonzalez, Rafael; Wang, Alan X

2016-12-01

In this paper, we described a new type of bioenabled nano-plasmonic sensors based on diatom photonic crystal biosilica with in-situ growth silver nanoparticles and demonstrated label-free chemical and biological sensing based on surface-enhanced Raman scattering (SERs) from complex samples. Diatoms are photosynthetic marine micro-organisms that create their own skeletal shells of hydrated amorphous silica, called frustules, which possess photonic crystal-like hierarchical micro- & nanoscale periodic pores. Our research shows that such hybrid plasmonic-biosilica nanostructures formed by cost-effective and eco-friendly bottom-up processes can achieve ultra-high limit of detection for medical applications, food sensing, water/air quality monitoring and geological/space research. The enhanced sensitivity comes from the optical coupling of the guided-mode resonance of the diatom frustules and the localized surface plasmons of the silver nanoparticles. Additionally, the nanoporous, ultra-hydrophilic diatom biosilica with large surface-to-volume ratio can concentrate more analyte molecules to the surface of the SERS substrates, which can help to detect biomolecules that cannot be easily adsorbed by metallic nanoparticles.

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

DOE PAGES

Mock, Thomas; Otillar, Robert P.; Strauss, Jan; ...

2017-01-26

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with allelesmore » that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.« less

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mock, Thomas; Otillar, Robert P.; Strauss, Jan

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with allelesmore » that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.« less

Electronic and geometrical properties of monoatomic and diatomic 2D honeycomb lattices. A DFT study

NASA Astrophysics Data System (ADS)

Rojas, Ángela; Rey, Rafael; Fonseca, Karen; Grupo de Óptica e Información Cuántica Team

Since the discovery of graphene by Geim and Novoselov at 2004, several analogous systems have been theoretically and experimentally studied, due to their technological interest. Both monoatomic lattices, such as silicine and germanene, and diatomic lattices (h-GaAs and h-GaN) have been studied. Using Density Functional Theory we obtain and confirm the chemical stability of these hexagonal 2D systems through the total energy curves as a function of interatomic distance. Unlike graphene, silicine and germanene, gapless materials, h-GaAs and h-GaN exhibit electronic gaps, different from that of the bulk, which could be interesting for the industry. On the other hand, the ab initio band structure calculations for graphene, silicene and germanene show a non-circular cross section around K points, at variance with the prediction of usual Tight-binding models. In fact, we have found that Dirac cones display a dihedral group symmetry. This implies that Fermi speed can change up to 30 % due to the orientation of the wave vector, for both electrons and holes. Traditional analytic studies use the Dirac equation for the electron dynamics at low energies. However, this equation assumes an isotropic, homogeneous and uniform space. Authors would like to thank the División de Investigación Sede Bogotá for their financial support at Universidad Nacional de Colombia. A. M. Rojas-Cuervo would also like to thank the Colciencias, Colombia.

Atmospheric deposition, water-quality, and sediment data for selected lakes in Mount Rainer, North Cascades, and Olympic National Parks, Washington, 2008-10

USGS Publications Warehouse

Sheibley, Rich W.; Foreman, James R.; Moran, Patrick W.; Swarzenski, Peter W.

2012-01-01

To evaluate the potential effect from atmospheric deposition of nitrogen to high-elevation lakes, the U.S. Geological Survey partnered with the National Park Service to develop a "critical load" of nitrogen for sediment diatoms. A critical load is defined as the level of a given pollutant (in this case, nitrogen) at which detrimental effects to a target endpoint (sediment diatoms) result. Because sediment diatoms are considered one of the "first responders" to ecosystem changes from nitrogen, they are a sensitive indicator for nitrogen deposition changes in natural areas. This report presents atmospheric deposition, water quality, sediment geochronology, and sediment diatom data collected from July 2008 through August 2010 in support of this effort.

Evidence for ubiquitous preferential particle orientation in representative oceanic shear flows.

PubMed

Nayak, Aditya R; McFarland, Malcolm N; Sullivan, James M; Twardowski, Michael S

2018-01-01

In situ measurements were undertaken to characterize particle fields in undisturbed oceanic environments. Simultaneous, co-located depth profiles of particle fields and flow characteristics were recorded using a submersible holographic imaging system and an acoustic Doppler velocimeter, under different flow conditions and varying particle concentration loads, typical of those found in coastal oceans and lakes. Nearly one million particles with major axis lengths ranging from ∼14 μm to 11.6 mm, representing diverse shapes, sizes, and aspect ratios were characterized as part of this study. The particle field consisted of marine snow, detrital matter, and phytoplankton, including colonial diatoms, which sometimes formed "thin layers" of high particle abundance. Clear evidence of preferential alignment of particles was seen at all sampling stations, where the orientation probability density function (PDF) peaked at near horizontal angles and coincided with regions of low velocity shear and weak turbulent dissipation rates. Furthermore, PDF values increased with increasing particle aspect ratios, in excellent agreement with models of spheroidal particle motion in simple shear flows. To the best of our knowledge, although preferential particle orientation in the ocean has been reported in two prior cases, our findings represent the first comprehensive field study examining this phenomenon. Evidence of nonrandom particle alignment in aquatic systems has significant consequences to aquatic optics theory and remote sensing, where perfectly random particle orientation and thus isotropic symmetry in optical parameters is assumed. Ecologically, chain-forming phytoplankton may have evolved to form large aspect ratio chains as a strategy to optimize light harvesting.

Evidence for ubiquitous preferential particle orientation in representative oceanic shear flows

PubMed Central

McFarland, Malcolm N.; Sullivan, James M.; Twardowski, Michael S.

2017-01-01

Abstract In situ measurements were undertaken to characterize particle fields in undisturbed oceanic environments. Simultaneous, co‐located depth profiles of particle fields and flow characteristics were recorded using a submersible holographic imaging system and an acoustic Doppler velocimeter, under different flow conditions and varying particle concentration loads, typical of those found in coastal oceans and lakes. Nearly one million particles with major axis lengths ranging from ∼14 μm to 11.6 mm, representing diverse shapes, sizes, and aspect ratios were characterized as part of this study. The particle field consisted of marine snow, detrital matter, and phytoplankton, including colonial diatoms, which sometimes formed “thin layers” of high particle abundance. Clear evidence of preferential alignment of particles was seen at all sampling stations, where the orientation probability density function (PDF) peaked at near horizontal angles and coincided with regions of low velocity shear and weak turbulent dissipation rates. Furthermore, PDF values increased with increasing particle aspect ratios, in excellent agreement with models of spheroidal particle motion in simple shear flows. To the best of our knowledge, although preferential particle orientation in the ocean has been reported in two prior cases, our findings represent the first comprehensive field study examining this phenomenon. Evidence of nonrandom particle alignment in aquatic systems has significant consequences to aquatic optics theory and remote sensing, where perfectly random particle orientation and thus isotropic symmetry in optical parameters is assumed. Ecologically, chain‐forming phytoplankton may have evolved to form large aspect ratio chains as a strategy to optimize light harvesting. PMID:29456268

[Environmental Hazards Assessment Program annual report, June 1992--June 1993]. Use of diatom distributions to monitor environmental health

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levine, R.H.

1993-12-01

A variety of approaches has been used in the past to assess the environmental impact of anthropogenic contaminants. One reliable index for aquatic environments is the analysis of diatom species distribution; the focus in this case being on the Savannah River. The completed objectives of this study were: (A) the development and use of procedures for measuring diatom distribution in the water column and (B) the development and evaluation of sediment sampling methods for retrospective analysis.

How-to-Do-It: Diatoms: The Ignored Alga in High School Biology.

ERIC Educational Resources Information Center

Hungerford, James J.

1988-01-01

Provides historical background, descriptions, uses and basis for identification of diatoms. Explains collection, dry-mount cleaning, and preparation procedures of the algae. Cites additional resources. (RT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diner, Rachel E.; Schwenck, Sarah M.; McCrow, John P.

Diatoms are a dominant group of eukaryotic phytoplankton that contribute substantially to global primary production and the cycling of important elements such as carbon and nitrogen. Heterotrophic bacteria, including members of the gammaproteobacteria, are commonly associated with diatom populations and may rely on them for organic carbon while potentially competing with them for other essential nutrients. Considering that bacterioplankton drive oceanic release of CO 2 (i.e., bacterial respiration) while diatoms drive ocean carbon sequestration vial the biological pump, the outcome of such competition could influence the direction and magnitude of carbon flux in the upper ocean. Nitrate availability is commonlymore » a determining factor for the growth of diatom populations, particularly in coastal and upwelling regions. Diatoms as well as many bacterial species can utilize nitrate, however the ability of bacteria to compete for nitrate may be hindered by carbon limitation. Here we have developed a genetically tractable model system using the pennate diatom Phaeodactylurn tricomuturn and the widespread heterotrophic bacteria Alterornonas macleodii to examine carbon-nitrogen dynamics. While subsisting solely on P. tricomutum derived carbon. A. macleodii does not appear to be an effective competitor for nitrate, and may in fact benefit the diatom; particularly in stationary phase. However, allochthonous dissolved organic carbon addition in the form of pyruvate triggers A. macleodii proliferation and nitrate uptake, leading to reduced P. tricornutum growth. Nitrate reductase deficient mutants of A. macleodii ( ΔnasA) do not exhibit such explosive growth and associated competitive ability in response to allochthonous carbon when nitrate is the sole nitrogen source, but could survive by utilizing solely P. tricomutum-derived nitrogen. Furthermore, allocthonous carbon addition enables wild-type A. macleodii to rescue nitrate reductase deficient P. tricomutum populations from nitrogen starvation, and RNA-seq transcriptomic evidence supports nitrogen-based interactions between diatoms and bacteria at the molecular level. As a result, this study provides key insights into the roles of carbon and nitrogen in phytoplankton-bacteria dynamics and lays the foundation for developing a mechanistic understanding of these interactions using co-culturing and genetic manipulation.« less

Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism.

PubMed

Matsuda, Yusuke; Hopkinson, Brian M; Nakajima, Kensuke; Dupont, Christopher L; Tsuji, Yoshinori

2017-09-05

Diatoms are one of the most successful marine eukaryotic algal groups, responsible for up to 20% of the annual global CO 2 fixation. The evolution of a CO 2 -concentrating mechanism (CCM) allowed diatoms to overcome a number of serious constraints on photosynthesis in the marine environment, particularly low [CO 2 ] aq in seawater relative to concentrations required by the CO 2 fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which is partly due to the slow diffusion rate of CO 2 in water and a limited CO 2 formation rate from [Formula: see text] in seawater. Diatoms use two alternative strategies to take up dissolved inorganic carbon (DIC) from the environment: one primarily relies on the direct uptake of [Formula: see text] through plasma-membrane type solute carrier (SLC) 4 family [Formula: see text] transporters and the other is more reliant on passive diffusion of CO 2 formed by an external carbonic anhydrase (CA). Bicarbonate taken up into the cytoplasm is most likely then actively transported into the chloroplast stroma by SLC4-type transporters on the chloroplast membrane system. Bicarbonate in the stroma is converted into CO 2 only in close proximity to RubisCO preventing unnecessary CO 2 leakage. CAs play significant roles in mobilizing DIC as it is progressively moved towards the site of fixation. However, the evolutionary types and subcellular locations of CAs are not conserved between different diatoms, strongly suggesting that this DIC mobilization strategy likely evolved multiple times with different origins. By contrast, the recent discovery of the thylakoid luminal θ-CA indicates that the strategy to supply CO 2 to RubisCO in the pyrenoid may be very similar to that of green algae, and strongly suggests convergent coevolution in CCM function of the thylakoid lumen not only among diatoms but among eukaryotic algae in general. In this review, both experimental and corresponding theoretical models of the diatom CCMs are discussed.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Diatom stratigraphy and long-term dissolved silica concentrations in the Baltic Sea

NASA Astrophysics Data System (ADS)

Olli, Kalle; Clarke, Annemarie; Danielsson, Åsa; Aigars, Juris; Conley, Daniel J.; Tamminen, Timo

2008-10-01

In many parts of the world coastal waters with anthropogenic eutrophication have experienced a gradual depletion of dissolved silica (DSi) stocks. This could put pressure on spring bloom diatom populations, e.g. by limiting the intensity of blooms or by causing shifts in species composition. In addition, eutrophication driven enhanced diatom growth is responsible for the redistribution of DSi from the water phase to the sediments, and changes in the growth conditions may be reflected in the sediment diatom stratigraphy. To test for changes in diatom communities we have analyzed four sediment cores from the Baltic Sea covering approximately the last 100 years. The sediment cores originate from the western Gulf of Finland, the Kattegat, the Baltic Proper and the Gulf of Riga. Three out of the four cores reveal only minor changes in composition of diatom assemblages, while the Gulf of Riga core contains major changes, occurring after the second World War. This area is set apart from the other Baltic Sea basins by a high frequency of low after spring bloom DSi concentrations (< 2 µmol L - 1 ) during a relatively well defined time period from 1991-1998. In 1991 to 1993 a rapid decline of DSi spring concentrations and winter stocks (down to 5 µmol L - 1 ) in the Gulf was preceded by exceptionally intense diatom spring blooms dominated by the heavily silicified species Thalassiosira baltica (1991-1992; up to 5.5 mg ww L - 1 ). T. baltica has been the principal spring bloom diatom in the Gulf of Riga since records began in 1975. DSi consumption and biomass yield experiments with cultured T. baltica suggest that intense blooms can potentially exhaust the DSi stock of the water column and exceed the annual Si dissolution in the Gulf of Riga. The phytoplankton time series reveals another exceptional T. baltica bloom period in 1981-1983 (up to 8 mg L - 1 ), which, however, took place before the regular DSi measurements. These periods may be reflected in the conspicuous accumulation of T. baltica frustules in the sediment core corresponding to ca. 1975-1985.

Response of diatoms and silicoflagellates to climate change in the Santa Barbara Basin during the past 250 years and the rise of the toxic diatom Pseudo-nitzschia australis

USGS Publications Warehouse

Barron, John A.; Bukry, David; Field, David B.; Finney, Bruce

2013-01-01

Diatoms and silicoflagellate assemblages were examined in two year-increments of varved samples spanning the interval from 1748 through 2007 in Santa Barbara Basin (SBB) box core SBBC0806 to determine the timing and impact of possible 20th century warming on several different components of the plankton. Diatoms (Thalassionema nitzschioides =TN) and silicoflagellates (Distephanus speculum s.l. =DS) indicative of cooler waters and a shallow thermocline begin to decline in the 1920s and persistently compose a lower percentage of the assemblage in the SBB by about 1940. Prior to 1940, TN constituted on average ~30% of the Chaetoceros-free diatom sediment assemblage and DS on average ~36% of the silicoflagellate assemblage. Between 1940 and 1996 these relative abundances were ~20% (TN) and ~8% (DS). These results are consistent with results from planktonic foraminifera and radiolarians that indicate an influence of 20th century warming on marine ecosystems before most scientific observations began. Cooling of surface waters coincident with the one of the strongest La Niña events of the 20th century (and a return to negative PDO conditions) in late 1998 brought about a return to pre-1940 values of these cool water taxa (TN ~31%, DS ~25%). However, this recent regional cooling appears to have been accompanied by profound changes in the diatom assemblage. Pseudo-nitzschia australis, and Pseudo-nitzschia multiseries, diatom species associated with domoic acid, a neurotoxin that causes shellfish poisoning and marine mammal deaths, rapidly became dominant in the SBB sediment record at the time of the regional cooling (1999) and increased substantially in numbers as a bloom-forming taxon (relative to Chaetoceros spores) in 2003. Prior to 2003 diatom blooms recorded in the SBB sediment record consisted predominantly of Chaetoceros spores and less commonly of Rhizosolenia-related species (Neocalyptrella robusta and R. setigera). Fecal pellets dominated by valves of P. australis, however, were particularly abundant in both the 2003 and 2006 samples, coincident with recorded incidents of domoic acid increase and widespread shellfish poisoning in the SBB.

Impact of iron on silicon utilization by diatoms in the Southern Ocean: A case study of Si/N cycle decoupling in a naturally iron-enriched area

NASA Astrophysics Data System (ADS)

Mosseri, Julie; Quéguiner, Bernard; Armand, Leanne; Cornet-Barthaux, Véronique

2008-03-01

Biogenic silica stocks and fluxes were investigated in austral summer over the naturally iron-fertilized Kerguelen Plateau and in nearby high-nutrient, low-chlorophyll (HNLC) off-plateau surface waters. The Kerguelen Plateau hosted a large-diatom bloom, with high levels of biogenic silica (BSi) but relatively low silicic acid (Si(OH) 4) uptake rates (1100±600 mmol m -2 and 8±4 mmol m -2 d -1, respectively). Diatoms of the naturally iron-enriched area presented high affinities for silicic acid, allowing them in combination with a beneficial nutrient vertical supply to grow in low silicic acid waters (<2 μM). Si(OH) 4 acid uptake rates were also compared with carbon and nitrogen uptake rates. As expected for diatoms growing in favourable nutrient conditions, and from previous artificial iron-enrichment experiments, Si:C and Si:NO 3 elemental uptake ratios of the natural diatom community of the plateau were close to 0.13 and 1, respectively. In contrast, diatom communities in the HNLC waters were composed of strongly silicified (high Si:C, Si:NO 3 uptake ratios) diatoms with low affinities for Si(OH) 4. Although the Si:NO 3 uptake ratio in the surface waters of the plateau was close to 1, the apparent consumption of nitrate on a seasonal basis was much lower (˜5 μM) than the apparent consumption of silicic acid (˜15 μM). This was mainly due to diatoms growing actively on ammonium (i.e. 39-77% of the total nitrogen uptake) produced by an intense heterotrophic activity. Thus we find that while Fe fertilization does increase N uptake with respect to Si uptake, rapid recycling of N decouples nitrogen and carbon export from silica export so that the "silicate pump" remains more efficient than that of N (or P). For this reason an iron-fertilized Southern Ocean is unlikely to experience nitrate exhaustion or export silicic acid to the global ocean.

The DANTE Boltzmann transport solver: An unstructured mesh, 3-D, spherical harmonics algorithm compatible with parallel computer architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGhee, J.M.; Roberts, R.M.; Morel, J.E.

1997-06-01

A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner formore » scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated.« less

Modelling UV irradiances on arbitrarily oriented surfaces: effects of sky obstructions

NASA Astrophysics Data System (ADS)

Hess, M.; Koepke, P.

2008-07-01

A method is presented to calculate UV irradiances on inclined surfaces that additionally takes into account the influence of sky obstructions caused by obstacles such as mountains, houses, trees, or umbrellas. With this method it is thus possible to calculate the impact of UV radiation on biological systems, such as, for instance, the human skin or eye, in any natural or artificial environment. The method, which consists of a combination of radiation models, is explained here and the accuracy of its results is demonstrated. The effect of a natural skyline is shown for an Alpine ski area, where the UV irradiance even on a horizontal surface may increase due to reflection from snow by more than 10 percent. In contrast, in a street canyon the irradiance on a horizontal surface is reduced to 30% in shadow and to about 75% for a position in the sun.

Electromagnetic fields radiated from a lightning return stroke - Application of an exact solution to Maxwell's equations

NASA Technical Reports Server (NTRS)

Le Vine, D. M.; Meneghini, R.

1978-01-01

A solution is presented for the electromagnetic fields radiated by an arbitrarily oriented current filament over a conducting ground plane in the case where the current propagates along the filament at the speed of light, and this solution is interpreted in terms of radiation from lightning return strokes. The solution is exact in the fullest sense; no mathematical approximations are made, and the governing differential equations and boundary conditions are satisfied. The solution has the additional attribute of being specified in closed form in terms of elementary functions. This solution is discussed from the point of view of deducing lightning current wave forms from measurements of the electromagnetic fields and understanding the effects of channel tortuosity on the radiated fields. In addition, it is compared with two approximate solutions, the traditional moment approximation and the Fraunhofer approximation, and a set of criteria describing their applicability are presented and interpreted.

A resolution measure for three-dimensional microscopy

PubMed Central

Chao, Jerry; Ram, Sripad; Abraham, Anish V.; Ward, E. Sally; Ober, Raimund J.

2009-01-01

A three-dimensional (3D) resolution measure for the conventional optical microscope is introduced which overcomes the drawbacks of the classical 3D (axial) resolution limit. Formulated within the context of a parameter estimation problem and based on the Cramer-Rao lower bound, this 3D resolution measure indicates the accuracy with which a given distance between two objects in 3D space can be determined from the acquired image. It predicts that, given enough photons from the objects of interest, arbitrarily small distances of separation can be estimated with prespecified accuracy. Using simulated images of point source pairs, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure. We also demonstrate how different factors, such as extraneous noise sources and the spatial orientation of the imaged object pair, can affect the accuracy with which a given distance of separation can be determined. PMID:20161040

Nanopatterning reconfigurable magnetic landscapes via thermally assisted scanning probe lithography

NASA Astrophysics Data System (ADS)

Albisetti, E.; Petti, D.; Pancaldi, M.; Madami, M.; Tacchi, S.; Curtis, J.; King, W. P.; Papp, A.; Csaba, G.; Porod, W.; Vavassori, P.; Riedo, E.; Bertacco, R.

2016-06-01

The search for novel tools to control magnetism at the nanoscale is crucial for the development of new paradigms in optics, electronics and spintronics. So far, the fabrication of magnetic nanostructures has been achieved mainly through irreversible structural or chemical modifications. Here, we propose a new concept for creating reconfigurable magnetic nanopatterns by crafting, at the nanoscale, the magnetic anisotropy landscape of a ferromagnetic layer exchange-coupled to an antiferromagnetic layer. By performing localized field cooling with the hot tip of a scanning probe microscope, magnetic structures, with arbitrarily oriented magnetization and tunable unidirectional anisotropy, are reversibly patterned without modifying the film chemistry and topography. This opens unforeseen possibilities for the development of novel metamaterials with finely tuned magnetic properties, such as reconfigurable magneto-plasmonic and magnonic crystals. In this context, we experimentally demonstrate spatially controlled spin wave excitation and propagation in magnetic structures patterned with the proposed method.

Nanopatterned reconfigurable spin-textures for magnonics

NASA Astrophysics Data System (ADS)

Albisetti, E.; Petti, D.; Pancaldi, M.; Madami, M.; Tacchi, S.; Curtis, J.; King, W. P.; Papp, A.; Csaba, G.; Porod, W.; Vavassori, P.; Riedo, E.; Bertacco, R.

The control of spin-waves holds the promise to enable energy-efficient information transport and wave-based computing. Conventionally, the engineering of spin-waves is achieved via physically patterning magnetic structures such as magnonic crystals and micro-nanowires. We demonstrate a new concept for creating reconfigurable magnonic nanostructures, by crafting at the nanoscale the magnetic anisotropy landscape of a ferromagnet exchange-coupled to an antiferromagnet. By performing a highly localized field cooling with the hot tip of a scanning probe microscope, magnetic structures, with arbitrarily oriented magnetization and tunable unidirectional anisotropy, are patterned without modifying the film chemistry and topography. We demonstrate that, in such structures, the spin-wave excitation and propagation can be spatially controlled at remanence, and can be tuned by external magnetic fields. This opens the way to the use of nanopatterned spin-textures, such as domains and domain walls, for exciting and manipulating magnons in reconfigurable nanocircuits. Partially funded by the EC through project SWING (no. 705326).

Nanopatterning reconfigurable magnetic landscapes via thermally assisted scanning probe lithography.

PubMed

Albisetti, E; Petti, D; Pancaldi, M; Madami, M; Tacchi, S; Curtis, J; King, W P; Papp, A; Csaba, G; Porod, W; Vavassori, P; Riedo, E; Bertacco, R

2016-06-01

The search for novel tools to control magnetism at the nanoscale is crucial for the development of new paradigms in optics, electronics and spintronics. So far, the fabrication of magnetic nanostructures has been achieved mainly through irreversible structural or chemical modifications. Here, we propose a new concept for creating reconfigurable magnetic nanopatterns by crafting, at the nanoscale, the magnetic anisotropy landscape of a ferromagnetic layer exchange-coupled to an antiferromagnetic layer. By performing localized field cooling with the hot tip of a scanning probe microscope, magnetic structures, with arbitrarily oriented magnetization and tunable unidirectional anisotropy, are reversibly patterned without modifying the film chemistry and topography. This opens unforeseen possibilities for the development of novel metamaterials with finely tuned magnetic properties, such as reconfigurable magneto-plasmonic and magnonic crystals. In this context, we experimentally demonstrate spatially controlled spin wave excitation and propagation in magnetic structures patterned with the proposed method.

A finite element solution algorithm for the Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Baker, A. J.

1974-01-01

A finite element solution algorithm is established for the two-dimensional Navier-Stokes equations governing the steady-state kinematics and thermodynamics of a variable viscosity, compressible multiple-species fluid. For an incompressible fluid, the motion may be transient as well. The primitive dependent variables are replaced by a vorticity-streamfunction description valid in domains spanned by rectangular, cylindrical and spherical coordinate systems. Use of derived variables provides a uniformly elliptic partial differential equation description for the Navier-Stokes system, and for which the finite element algorithm is established. Explicit non-linearity is accepted by the theory, since no psuedo-variational principles are employed, and there is no requirement for either computational mesh or solution domain closure regularity. Boundary condition constraints on the normal flux and tangential distribution of all computational variables, as well as velocity, are routinely piecewise enforceable on domain closure segments arbitrarily oriented with respect to a global reference frame.

User's guide to computer program CIVM-JET 4B to calculate the transient structural responses of partial and/or complete structural rings to engine-rotor-fragment impact

NASA Technical Reports Server (NTRS)

Stagliano, T. R.; Spilker, R. L.; Witmer, E. A.

1976-01-01

A user-oriented computer program CIVM-JET 4B is described to predict the large-deflection elastic-plastic structural responses of fragment impacted single-layer: (a) partial-ring fragment containment or deflector structure or (b) complete-ring fragment containment structure. These two types of structures may be either free or supported in various ways. Supports accommodated include: (1) point supports such as pinned-fixed, ideally-clamped, or supported by a structural branch simulating mounting-bracket structure and (2) elastic foundation support distributed over selected regions of the structure. The initial geometry of each partial or complete ring may be circular or arbitrarily curved; uniform or variable thicknesses of the structure are accommodated. The structural material is assumed to be initially isotropic; strain hardening and strain rate effects are taken into account.

An integral equation formulation for rigid bodies in Stokes flow in three dimensions

NASA Astrophysics Data System (ADS)

Corona, Eduardo; Greengard, Leslie; Rachh, Manas; Veerapaneni, Shravan

2017-03-01

We present a new derivation of a boundary integral equation (BIE) for simulating the three-dimensional dynamics of arbitrarily-shaped rigid particles of genus zero immersed in a Stokes fluid, on which are prescribed forces and torques. Our method is based on a single-layer representation and leads to a simple second-kind integral equation. It avoids the use of auxiliary sources within each particle that play a role in some classical formulations. We use a spectrally accurate quadrature scheme to evaluate the corresponding layer potentials, so that only a small number of spatial discretization points per particle are required. The resulting discrete sums are computed in O (n) time, where n denotes the number of particles, using the fast multipole method (FMM). The particle positions and orientations are updated by a high-order time-stepping scheme. We illustrate the accuracy, conditioning and scaling of our solvers with several numerical examples.

Fundamental analysis of the failure of polymer-based fiber reinforced composites

NASA Technical Reports Server (NTRS)

Kanninen, M. F.; Rybicki, E. F.; Griffith, W. I.; Broek, D.

1975-01-01

A mathematical model predicting the strength of unidirectional fiber reinforced composites containing known flaws and with linear elastic-brittle material behavior was developed. The approach was to imbed a local heterogeneous region surrounding the crack tip into an anisotropic elastic continuum. This (1) permits an explicit analysis of the micromechanical processes involved in the fracture, and (2) remains simple enough to be useful in practical computations. Computations for arbitrary flaw size and orientation under arbitrary applied loads were performed. The mechanical properties were those of graphite epoxy. With the rupture properties arbitrarily varied to test the capabilities of the model to reflect real fracture modes, it was shown that fiber breakage, matrix crazing, crack bridging, matrix-fiber debonding, and axial splitting can all occur during a period of (gradually) increasing load prior to catastrophic failure. The calculations also reveal the sequential nature of the stable crack growth process proceding fracture.

Design and spacecraft-integration of RTGs for solar probe

NASA Technical Reports Server (NTRS)

Schock, A.; Noravian, H.; Or, T.; Sankarankandath, V.

1990-01-01

The design, analysis, and spacecraft integration of radioisotope thermoelectric generators (RTG) to power the Solar Probe under study at NASA JPL is described. The mission of the Solar Probe is to explore the solar corona by performing in situ measurements at up to four solar radii to the sun. Design constraints for the RTG are discussed. The chief challenge in the design and system integration of the Solar Probe's RTG is a heat rejection problem. Two RTG orientations, horizontal and oblique, are analyzed for effectiveness and results are summarized in chart form. A number of cooling strategies are also investigated, including heat-pipe and reflector-cooled options. A methodology and general computer code are presented for analyzing the performance of arbitrarily obstructed RTGs with both axial and circumferential temperature, voltage, and current variation. This methodology is applied to the specific example of the Solar Probe RTG obstructed by a semicylindrical reflector of 15-inch radius.

Simulation of radiation from lightning return strokes - The effects of tortuosity

NASA Technical Reports Server (NTRS)

Levine, D. M.; Meneghini, R.

1978-01-01

A Monte Carlo simulation has been developed for the electromagnetic fields radiated from a tortuous lightning channel. This was done using a piecewise linear model for the channel and employing for each element the field radiated by a traveling wave on an arbitrarily oriented filament over a conducting plane. The simulation reproduces experimental data reasonably well and has been used to study the effects of tortuosity on the fields radiated by return strokes. Tortuosity can significantly modify the radiated waveform, tending to render it less representative of the current pulse and more nearly unipolar than one would expect based on the theory for a long straight channel. In the frequency domain the effect of tortuosity is an increase in high frequency energy as compared with an equivalent straight channel. The extent of this increase depends on the mean length of the elements comprising the channel and can be significant.

Finite element solution for energy conservation using a highly stable explicit integration algorithm

NASA Technical Reports Server (NTRS)

Baker, A. J.; Manhardt, P. D.

1972-01-01

Theoretical derivation of a finite element solution algorithm for the transient energy conservation equation in multidimensional, stationary multi-media continua with irregular solution domain closure is considered. The complete finite element matrix forms for arbitrarily irregular discretizations are established, using natural coordinate function representations. The algorithm is embodied into a user-oriented computer program (COMOC) which obtains transient temperature distributions at the node points of the finite element discretization using a highly stable explicit integration procedure with automatic error control features. The finite element algorithm is shown to posses convergence with discretization for a transient sample problem. The condensed form for the specific heat element matrix is shown to be preferable to the consistent form. Computed results for diverse problems illustrate the versatility of COMOC, and easily prepared output subroutines are shown to allow quick engineering assessment of solution behavior.

Hydraulic containment: analytical and semi-analytical models for capture zone curve delineation

NASA Astrophysics Data System (ADS)

Christ, John A.; Goltz, Mark N.

2002-05-01

We present an efficient semi-analytical algorithm that uses complex potential theory and superposition to delineate the capture zone curves of extraction wells. This algorithm is more flexible than previously published techniques and allows the user to determine the capture zone for a number of arbitrarily positioned extraction wells pumping at different rates. The algorithm is applied to determine the capture zones and optimal well spacing of two wells pumping at different flow rates and positioned at various orientations to the direction of regional groundwater flow. The algorithm is also applied to determine capture zones for non-colinear three-well configurations as well as to determine optimal well spacing for up to six wells pumping at the same rate. We show that the optimal well spacing is found by minimizing the difference in the stream function evaluated at the stagnation points.

Comparison of arbitrarily primed PCR and macrorestriction (pulsed-field gel electrophoresis) typing of Pseudomonas aeruginosa strains from cystic fibrosis patients.

PubMed Central

Kersulyte, D; Struelens, M J; Deplano, A; Berg, D E

1995-01-01

Arbitrarily primed PCR fingerprinting was carried out on 43 Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients. Seventeen major groups of strains that coincided with groups also distinguished by macrorestriction (pulsed-field gel electrophoresis) typing were identified. Our results illustrated that a CF patient can carry more than one strain and can carry a given strain for long periods of time and that strains can evolve by changes in drug resistance or other phenotypic traits during long-term colonization. The arbitrarily primed PCR method is recommended for first-pass screening of P. aeruginosa isolates from CF patients, especially when many strains are to be typed, because of its sensitivity and efficiency. PMID:7559985

Establishing the Ecological Status of Mining-Impacted Freshwaters from Abrud River Catchment Area Using Benthic Diatom Communities (Ros, ia MontanÄă, Romania)

NASA Astrophysics Data System (ADS)

Olenici, Adriana; Baciu, Calin; Momeu, Laura; Cozma, Alexandra; Brahaita, Dorian; Pop, Cristian; Lazar, Laura; Popita, Gabriela; Teodosiu, Gabriela

2015-04-01

Keywords: diatom communities, indicator species, mine waters, water quality, Romania. Diatoms are a very distinct group of algae, identifiable under the light microscope by their yellow - brown coloration and by the presence of a thick silica cell wall. The potential for freshwater organisms to reflect changes in environmental conditions was first noted by Kolenati (1848) and Cohn (1853), who observed that biota in polluted waters were different from those in non-polluted situations. Diatoms are widely used to monitor river pollution because they are sensitive to water chemistry, especially to ionic content, pH, dissolved organic matter and nutrients. Wide geographic distribution and well-studied ecology of most diatom species are mentioned as major advantages of using diatoms as indicator organisms. At the same time water quality has begun to deteriorate increasingly, mainly as a result of the physical, chemical and bacteriological alterations, and the aquatic ecosystems are evermore affected by various types of pollution, the anthropic one being almost always included. A good example is Abrud River and its main tributaries (Roșia Montană and surrounding areas, Romania), which has suffered along the years because of the mining waters discharge. In this context, this study presents data on benthic diatom communities from the Abrud River catchment area. Sixteen sites have been sampled seasonal and the best represented diatom genera were Navicula, Nitzschia, Cymbella, Gomphonema, Achnantes, Surirella and Fragilaria. Qualitatively, the number of diatom species exhibited significant variation among sampling sites, also suggesting seasonal dynamics. For instance, in some sampling sites, algal assemblages were absent, as diatom communities were strongly affected by acid mine waters, released from old mining works and waste rocks depots. Some dominant taxa have been observed as well, suggesting critical saprobic levels of the Abrud River and some of its tributaries. The large quantity of organic matter, originating from untreated municipal water, together with the high concentrations of NO3-, draw attention to the mediocre quality of water in the area. Moreover, the values of the measured physical and chemical parameters (i.e. pH, salinity, conductivity, O2) and the concentrations of SO42-, Fe, Pb, Ni, Cu, Cd and Zn also indicates quality alterations caused by the mine waters flowing into some tributaries and the river. Besides diatoms, the study also referrs to the determination of bacterial communities existing in the same sampling area, that revealed the presence of the main groups of microorganisms involved in the biogeochemical cycles of C, N, Fe and S, and the absence of pathogenic bacteria such as total and faecal coliforms and faecal streptococci. The heterotrophic bacteria strains obtained which are highly adapted to the heavy metals occuring in the investigated habitats could be used as new microorganisms in the bioremediation processes of this water resource in future studies. Acknowledgments: The present contribution was financially supported by a grant of the Romanian National Authority for Scientific Research, CCCDI - UEFISCDI, project 3-005 Tools for sustainable gold mining in EU (SUSMIN). Dorian Brahaita has benefited from the financial support provided by the project POSDRU/159/1.5/S/132400.

The late Cenozoic diatom stratigraphy and paleolimnology of Tule Lake, Siskiyou Co. California

USGS Publications Warehouse

Bradbury, J.P.

1991-01-01

Lacustrine diatoms are diverse, well preserved and abundant in cores of lake sediment to 334 m depth near the town of Tulelake, Siskiyou County, northern California. The cores have been dated by radiometric, tephrochronologic and paleomagnetic techniques, which indicate a basal age of about 3 million years (Ma) and a nearly continuous depositional record for the Tule Lake basin for the last 3 million years (My). Fossil diatoms document the late Cenozoic paleolimnologic and paleoclimatic history for the northwestern edge of the Basin and Range Province. During the last 3 My, Tule Lake was typically a relatively deep, extensive lake. The Pliocene is characterized by a diatom flora dominated by Aulacoseira solida suggesting more abundant summer precipitation and warmer winters. Increases in 'Fragilaria' at 2.4 Ma and between 2.0 and 1.7 Ma imply cooler summers that correlate to glacial environments recorded elsewhere in the world. Stephanodiscus niagarae and 'Fragilaria' species dominate the Pleistocene. Benthic diatoms of alkalineenriched, saline waters occur with S. niagarae between 100 and 40 m depth (0.90-0.14 Ma). Tephrochronology indicates slow deposition and possible hiatuses between about 0.6 and 0.2 Ma. Overall, the Pleistocene diatom flora reflects cooler and sometimes drier climates, especially after major glaciations began 0.85 Ma. The chronology of even-numbered oxygen isotope stages approximately matches fluctuations in the abundance in 'Fragilaria' species since 1 Ma, suggesting that glacial periods at Tule Lake were expressed by relatively cool summers with enhanced effective moisture. Interglacial periods are represented by variable mixtures of freshwater planktonic and benthic alkaline diatom assemblages that suggest seasonal environments with winter-spring precipitation and summer moisture deficits. Glacial-interglacial environments since 150 ka were distinct from, and more variable than, those occurring earlier. The last full glacial period was very dry. Aulacoseira ambigua characterizes the late glacial and early Holocene record of Tule Lake. Its distribution indicates that warmer and wetter climates began about 15 ka in this part of the Great Basin. Fluctuations in diatom concentration suggests a 41000-yr. cycle between 3.0 and 2.5 Ma and 100000-yr. cycles after 1.0 Ma. In the late Pliocene and early Pleistocene, Aulacoseira solida percentages wax and wane in an approximately 400000-yr. cycle. The apparent response of Tule Lake diatom communities to orbitally induced insolation cycles underscores the importance of this record for the study of late Cenozoic paleoclimate change. The diatom stratigraphy records the evolution and local extinction of several species that may be biochronologically important. Stephanodiscus niagarae first appeared and became common in the Tule Lake record shortly after 1.8 Ma. Stephanodiscus carconensis disappeared about 1.8 Ma, while Aulacoseira solida is rare in the core after about 1.35 Ma. Cyclotella elgeri, a diatom characteristic of some outcrops referred to the Yonna Formation (Pliocene), is common only near the base of the core at an age of about 3 Ma. Detection of local extinctions is complicated by reworking of distinctive species from Pliocene diatomites surrounding Tule Lake. A new species, Aulacoseira paucistriata, is described from Pliocene lake deposits in the Klamath Basin. ?? 1991 Kluwer Academic Publishers.

Study on the effects of Ga-2N high co-doping and preferred orientation on the stability, bandgap and absorption spectrum of ZnO

NASA Astrophysics Data System (ADS)

Hou, Qing-Yu; Li, Wen-Cai; Qu, Ling-Feng; Zhao, Chun-Wang

2017-06-01

Currently, the stability and visible light properties of Ga-2N co-doped ZnO systems have been studied extensively by experimental analysis and theoretical calculations. However, previous theoretical calculations arbitrarily assigned Ga- and 2N-doped sites in ZnO. In addition, the most stable and possible doping orientations of doped systems have not been fully and systematically considered. Therefore, in this paper, the electron structure and absorption spectra of the unit cells of doped and pure systems were calculated by first-principles plane-wave ultrasoft pseudopotential with the GGA+U method. Calculations were performed for pure ZnO, Ga-2N supercells heavily co-doped with Zn1-xGaxO1-yNy (x = 0.03125 - 0.0625, y = 0.0625 - 0.125) under different co-doping orientations and conditions, and the Zn16GaN2O14 interstitial model. The results indicated that under different orientations and constant Ga-2N co-doping concentrations, the systems co-doped with Ga-N atoms vertically oriented to the c-axis and with another N atom located in the nearest-neighboring site exhibited higher stability over the others, thus lowering formation energy and facilitating doping. Moreover, Ga-interstitial- and 2N-co-doped ZnO systems easily formed chemical compounds. Increasing co-doping concentration while the co-doping method remained constant decreased doped system volume and lowered formation energies. Meantime, co-doped systems were more stable and doping was facilitated. The bandgap was also narrower and red shifting of the absorption spectrum was more significant. These results agreed with previously reported experimental results. In addition, the absorption spectra of Ga-interstitial- and 2N-co-doped ZnO both blue shifted in the UV region compared with that of the pure ZnO system.

Phytoplankton Community Structure in 2011-2013 Compared to the Extratropical Warming Event of 2014-2015

NASA Astrophysics Data System (ADS)

Du, X.; Peterson, W. T.

2018-02-01

Coastal waters of the Northern California Current experienced "normal" ocean conditions in 2011-2012, weak upwelling in 2013-2014, then suddenly warmed in September 2014. The response of phytoplankton community structure to contrasting ocean conditions was determined from samples collected off Newport, Oregon. Cluster analysis identified three prominent phytoplankton community types: one that occurred during the upwelling season characterized by the highest abundance and diversity of diatoms, a preupwelling/relaxation community characterized by lower abundance, lowest diversity of diatoms and dinoflagellates, and another one associated with the warm anomalies from September 2014 through 2015 with reduced diatom abundance and diversity but the highest dinoflagellate diversity. The changes of diatom and dinoflagellate community were correlated with local factors (silicate, silicate: nitrate ratios, temperature, and salinity), and with the Pacific Decadal Oscillation.

Isolation and Physiological Characterization of a Novel Algicidal Virus Infecting the Marine Diatom Skeletonema costatum.

PubMed

Kim, JinJoo; Kim, Chang-Hoon; Youn, Seok-Hyun; Choi, Tae-Jin

2015-06-01

Diatoms are a major component of the biological community, serving as the principal primary producers in the food web and sustaining oxygen levels in aquatic environments. Among marine planktonic diatoms, the cosmopolitan Skeletonema costatum is one of the most abundant and widespread species in the world's oceans. Here, we report the basic characteristics of a new diatom-infecting S. costatum virus (ScosV) isolated from Jaran Bay, Korea, in June 2008. ScosV is a polyhedral virus (45-50 nm in diameter) that propagates in the cytoplasm of host cells and causes lysis of S. costatum cultures. The infectivity of ScosV was determined to be strain- rather than species-specific, similar to other algal viruses. The burst size and latent period were roughly estimated at 90-250 infectious units/cell and <48 h, respectively.

Binding Structures of Diatomic Molecules to Co-Porphyrins on Au(111) Studied by Scanning Tunneling Microscopy

NASA Astrophysics Data System (ADS)

Lee, Soon-Hyeong; Chang, Yun; Kim, Howon; Jang, Won; Kim, Yong-Hyun; Kahng, Se-Jong; Department Of Physics, Korea University. Collaboration; Graduate School Of Nanoscience; Technology (Wcu), Kaist Collaboration

2013-03-01

Axial bindings of diatomic molecules to metalloporphyrins involve in the dynamic processes of biological functions such as respiration, neurotransmission, and photosynthesis. The binding reactions are also useful in sensor applications and to control molecular spins in metalloporphyrins for spintronic applications. Here, we present the binding structures of diatomic molecules to surface-supported Co-porphyrins studied using scanning tunneling microscopy. Upon gas exposure, three-lobed structures of Co-porphyrins transformed to bright ring shapes on Au(111), whereas H2-porphyrins of dark rings remained intact. The bright rings are explained by the structures of reaction complexes where a diatomic ligand, tilted away from the axis normal to the porphyrin plane, is under precession. Our results are consistent with previous bulk experiments using X-ray diffraction and nuclear magnetic resonance spectroscopy.

Diatom-sedimentation feedback generates a self-organized geomorphic landscape on intertidal mudflats (Invited)

NASA Astrophysics Data System (ADS)

van de Koppel, J.; Weerman, E.; Herman, P.

2010-12-01

During spring, intertidal flats can exhibit strikingly regular spatial patterns of diatom-covered hummocks alternating with almost bare, water-filled hollows. We hypothesize that 1) the formation of this geomorphic landscape is caused by a strong interaction between benthic diatoms and sediment dynamics, inducing spatial self-organization, and 2) that self-organization affects ecosystem functioning by increasing the net average sedimentation on the tidal flat. We present a combined empirical and mathematical study to test the first hypothesis. We determined how the sediment erosion threshold varied with diatom cover and elevation. Our results were incorporated into a mathematical model to investigate whether the proposed mechanism could explain the formation of the observed patterns. Our mathematical model confirmed that the interaction between sedimentation, diatom growth and water redistribution could induce the formation of regular patterns on the intertidal mudflat. The model predicts that areas exhibiting spatially-self-organized patterns have increased sediment accretion and diatom biomass compared with areas lacking spatial patterns. We tested this prediction by following the sediment elevation during the season on both patterned and unpatterned parts of the mudflat. The results of our study confirmed our model prediction, as more sediment was found to accumulate in patterned parts of the mudflat, revealing how self-organization affected the functioning of mudflat ecosystems. Our study on intertidal mudflats provides a simple but clear-cut example of how the interaction between biological and geomorphological processes, through the process of self-organization, induces a self-organized geomorphic landscape.

A size-specific record of diatom-bound organic carbon isotopes over the Eocene/Oligocene boundary

NASA Astrophysics Data System (ADS)

Heureux, Ana; Rickaby, Ros; Hermoso, Michael; Lee, Renee

2013-04-01

Marine diatoms, ubiquitous silicifying photosynthetic algae, are major contributors to marine primary production in the modern ocean. In all primary producers, the enzyme Rubisco catalyzes the fixation of carbon from CO2. Due to the low concentration and slow diffusion rates of CO2 as a substrate in naturally buffered seawater, most marine algae have evolved mechanisms for concentrating CO2 around the Rubisco enzyme. The efficiency of these carbon concentration mechanisms may be reflected in the carbon isotopes of organic matter preserved within sedimentary nannofossils, and is hypothesized to change in response to ambient CO2 concentration. As a first order investigation into the relationship between carbon concentration related to cell size and isotopic fractionation of carbon into organic matter, or ɛp, in response to changes in CO2, we have created a novel record from IODP site 1090 in the Atlantic sector of the Southern Ocean, spanning the marked temperature and gradual pCO2 decline across the Eocene/Oligocene boundary. Using size microseparation of diatom silica and established cleaning techniques to isolate organic material trapped inside the diatom frustules, this record provides a size fraction-specific account of ɛp from marine diatoms. Comparing these individual records with the bulk diatom record from this site elucidates the potential effects of size related carbon concentration on trends in ɛp across the E/O boundary and may reveal further insight into the magnitude of CO2 decline.

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

PubMed Central

Parks, Matthew B; Wickett, Norman J; Alverson, Andrew J

2018-01-01

Abstract Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available. PMID:29040712

Potential of diatom consortium developed by nutrient enrichment for biodiesel production and simultaneous nutrient removal from waste water.

PubMed

Marella, Thomas Kiran; Parine, Narasimha Reddy; Tiwari, Archana

2018-05-01

Because of the decreasing fossil fuel supply and increasing greenhouse gas (GHG) emissions, microalgae have been identified as a viable and sustainable feedstock for biofuel production. The major effect of the release of wastewater rich in organic compounds has led to the eutrophication of freshwater ecosystems. A combined approach of freshwater diatom cultivation with urban sewage water treatment is a promising solution for nutrient removal and biofuel production. In this study, urban wastewater from eutrophic Hussain Sagar Lake was used to cultivate a diatom algae consortium, and the effects of silica and trace metal enrichment on growth, nutrient removal, and lipid production were evaluated. The nano-silica-based micronutrient mixture Nualgi containing Si, Fe, and metal ions was used to optimize diatom growth. Respectively, N and P reductions of 95.1% and 88.9%, COD and BOD reductions of 91% and 51% with a biomass yield of 122.5 mg L -1  day -1 and lipid productivity of 37 mg L -1  day -1 were observed for cultures grown in waste water using Nualgi. Fatty acid profiles revealed 13 different fatty acids with slight differences in their percentage of dry cell weight (DCW) depending on enrichment level. These results demonstrate the potential of diatom algae grown in wastewater to produce feedstock for renewable biodiesel production. Enhanced carbon and excess nutrient utilization makes diatoms ideal candidates for co-processes such as CO 2 sequestration, biodiesel production, and wastewater phycoremediation.

Establishing ecological reference conditions and tracking post-application effectiveness of lanthanum-saturated bentonite clay (Phoslock®) for reducing phosphorus in aquatic systems: an applied paleolimnological approach.

PubMed

Moos, M T; Taffs, K H; Longstaff, B J; Ginn, B K

2014-08-01

Innovative management strategies for nutrient enrichment of freshwater are important in the face of this increasing global problem, however many strategies are not assessed over long enough time periods to establish effectiveness. Paleolimnological techniques using diatoms as biological indicators were utilized to establish ecological reference conditions, environmental variation, and the effectiveness of lanthanum-saturated bentonite clay (brand name: Phoslock(®)) applied to reduce water column phosphorus (P) concentrations in four waterbodies in Ontario, Canada, and eastern Australia. In sediment cores from the two Canadian sites, there were short-lived changes to diatom assemblages, relative to inferred background conditions, and a temporary reduction in both measured and diatom-inferred total phosphorus (TP) before returning to pre-application conditions (particularly in the urban stormwater management pond which has a high flushing rate and responds rapidly to precipitation and surface run-off). The two Australian sites (a sewage treatment pond and a shallow recreational lake), recorded no reduction in diatom-inferred TP. Based on our pre-application environmental reconstruction, changes to the diatom assemblages and diatom-inferred TP appeared to be driven by larger, climatic factors. While laboratory tests involving this product showed sharp reductions in water column TP, management strategies require detailed information on pre-application environmental conditions and variations in order to accurately assess the effectiveness of new technologies for lake management. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal

PubMed Central

Zakharova, Yulia R.; Galachyants, Yuri P.; Kurilkina, Maria I.; Likhoshvay, Alexander V.; Petrova, Darya P.; Shishlyannikov, Sergey M.; Ravin, Nikolai V.; Mardanov, Andrey V.; Beletsky, Alexey V.; Likhoshway, Yelena V.

2013-01-01

Insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. Using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the cell. The structure of microbial community in the near-bottom water layer has been characterized by pyrosequencing of the 16S rRNA gene, which has revealed 149 208 unique sequences. According to the results of metagenomic analysis, the community is dominated by representatives of Proteobacteria (41.9%), Actinobacteria (16%); then follow Acidobacteria (6.9%), Cyanobacteria (5%), Bacteroidetes (4.7%), Firmicutes (2.8%), Nitrospira (1.6%), and Verrucomicrobia (1%); other phylotypes account for less than 1% each. For 18.7% of the sequences, taxonomic identification has been possible only to the Bacteria domain level. Many bacteria identified to the genus level have close relatives occurring in other aquatic ecosystems and soils. The metagenome of the bacterial community from the near-bottom water layer also contains 16S rRNA gene sequences found in previously isolated bacterial strains possessing hydrolytic enzyme activity. These data show that potential degraders of diatoms occur among the vast variety of microorganisms in the near-bottom water of Lake Baikal. PMID:23560063

Santa Barbara Basin diatom and silicoflagellate response to global climate anomalies during the past 2200 years

USGS Publications Warehouse

Barron, J.A.; Bukry, D.; Field, D.

2010-01-01

Santa Barbara Basin (SBB) diatom and silicoflagellate assemblages are quantified from a box core record spanning AD 1940-2001 and an Ocean Drilling Program Hole 893A record from ???220 BC to AD 1880. The combined relative abundance of the diatoms Fragilariopsis doliolus and Nitzschia interrupteseriata from continuous two-year sampling intervals in the box core varies with sea surface temperature (SST), suggesting its utility in SST reconstruction. The assemblage data from the ODP 893A record indicate a broad interval of generally cooler SSTs between ???AD 800 and 1350, which corresponds to the Medieval Climate Anomaly (MCA), a period of generally warmer temperatures across other regions of the northern hemisphere. The assemblages also indicate an interval of generally warmer SSTs between ???AD 1400 and 1800, a period of otherwise global cooling referred to as the Little Ice Age (LIA). The changes in assemblages of diatoms and silicoflagellates support the hypothesis that the widespread droughts of the Medieval Climate Anomaly in the Western US were associated with cooler eastern North Pacific SST. The box core assemblages have higher percentages of tropical and subtropical compared to temperate and subpolar species than the ODP samples, reflecting a response of phytoplankton communities to an unusual 20th century warming. Pseudonitzschia australis, a diatom linked with domoic acid production, begins to become more common (>3% of the diatom assemblage) in the box core only after AD 1985, suggesting a link to anthropogenic activity. ?? 2008 Elsevier Ltd and INQUA.

Heliotropism in modern stromatolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awramik, S.M.

1985-01-01

Three different examples of modern microbial mats and stromatolites have been discovered that exhibit a preferred orientation towards specular sunlight. In Hamelin Pool of Shark Bay, Western Australia, subtidal decimeter-sized discrete columns and intertidal centimeter-sized tufts were found pointing north. In thermal spring effluents and pools of Yellowstone National Park, columnar and conical centimeter-sized microbial structures were found to be inclined to the south. None of these inclined structures show growth orientation in response to prevailing fluid directions. Each example occurs in markedly different environments and each has different photosynthetic microbes: (1) the subtidal Shark Bay columns are dominated bymore » surficial diatoms: (2) the intertidal Shark Bay tufts constructed by a filamentous cyanobacterium; and (3) the cones and columns in Yellowstone are built by filamentous flexibacteria and cyanobacteria. Sunlight must be considered a major driving force in stromatolite morphogenesis. Extrapolation of these modern heliotropic columnar stromatolites to fossil examples supports the paleolatitude hypothesis of Vologdin (1961) and of Nordeng (1963) and the days per year hypothesis of Vanyo and Awramik (1982). Taken together, and especially when combined with paleomagnetic analyses, the procedures yield an impressive array of data on Earth and Earth-Sun-Moon histories.« less

Attosecond polarization control in atomic RABBITT-like experiments assisted by a circularly polarized laser

NASA Astrophysics Data System (ADS)

Boll, D. I. R.; Fojón, O. A.

2017-12-01

We study theoretically the single ionization of noble gas atoms by the combined action of an attosecond pulse train with linear polarization and an assistant laser field with circular polarization. We employ a non-perturbative model that under certain approximations gives closed-form expressions for the angular distributions of photoelectrons. Interestingly, our model allow us to interpret these angular distributions as two-centre interferences where the orientation and the modulus of the separation vector between the virtual emitters is governed by the assistant laser field. Additionally, we show that such a configuration of light fields is similar to the polarization control technique, where both the attosecond pulse train and the assistant laser field have linear polarizations whose relative orientation may be controlled. Moreover, in order to compare our results with the available experimental data, we obtain analytical expressions for the cross sections integrated over the photoelectron emission angles. By means of these expressions, we define the ‘magic time’ as the delay for which the total cross sections for atomic targets exhibit the same functional form as the one of the monochromatic photoionization of diatomic molecular targets.

An unusual early Holocene diatom event north of the Getz Ice Shelf (Amundsen Sea): Implications for West Antarctic Ice Sheet development

NASA Astrophysics Data System (ADS)

Esper, O.; Gersonde, R.; Hillenbrand, C.; Kuhn, G.; Smith, J.

2011-12-01

Modern global change affects not only the polar north but also, and to increasing extent, the southern high latitudes, especially the Antarctic regions covered by the West Antarctic Ice Sheet (WAIS). Consequently, knowledge of the mechanisms controlling past WAIS dynamics and WAIS behaviour at the last deglaciation is critical to predict its development in a future warming world. Geological and palaeobiological information from major drainage areas of the WAIS, like the Amundsen Sea Embayment, shed light on the history of the WAIS glaciers. Sediment records obtained from a deep inner shelf basin north of Getz Ice Shelf document a deglacial warming in three phases. Above a glacial diamicton and a sediment package barren of microfossils that document sediment deposition by grounded ice and below an ice shelf or perennial sea ice cover (possibly fast ice), respectively, a sediment section with diatom assemblages dominated by sea ice taxa indicates ice shelf retreat and seasonal ice-free conditions. This conclusion is supported by diatom-based summer temperature reconstructions. The early retreat was followed by a phase, when exceptional diatom ooze was deposited around 12,500 cal. years B.P. [1]. Microscopical inspection of this ooze revealed excellent preservation of diatom frustules of the species Corethron pennatum together with vegetative Chaetoceros, thus an assemblage usually not preserved in the sedimentary record. Sediments succeeding this section contain diatom assemblages indicating rather constant Holocene cold water conditions with seasonal sea ice. The deposition of the diatom ooze can be related to changes in hydrographic conditions including strong advection of nutrients. However, sediment focussing in the partly steep inner shelf basins cannot be excluded as a factor enhancing the thickness of the ooze deposits. It is not only the presence of the diatom ooze but also the exceptional preservation and the species composition of the diatom assemblage, which point to specific scenarios involving e.g. changes in the food web that can be related to warmer surface water temperatures. Such warming of shelf waters may be related with an overshooting Atlantic Meridional Overturning Circulation (AMOC) and strong injection of warmer North Atlantic Deep Water into the Southern Ocean water masses at Termination I as reported by [2]. Such finding may highlight the effects of AMOC changes on Antarctic ice shelf extent and coastal ecosystems. [1] Hillenbrand et al., 2010. J. Quat. Sci. 25 (3), 280-295. [2] Barker et al., 2010. Nature Geosci. 3, 567-571.

Combination of geochemical and hydrobiological tracers for the analysis of runoff generating processes in a lowland catchment

NASA Astrophysics Data System (ADS)

Faber, Claas; Wu, Naicheng; Ulrich, Uta; Fohrer, Nicola

2015-04-01

Since lowlands are characterised by flat topography and low hydraulic gradients, groundwater inflow has a large influence to streamflow generation in such catchments. In catchments with intense agricultural land use, artificial drainages are often another major contributor to streamflow. They shorten the soil passage and thus change the matter retention potential as well as runoff dynamics of a catchment. Contribution of surface runoff to streamflow is usually less important in volume. However, due to high concentrations of agrochemicals, surface runoff can constitute an important entry pathway into water bodies, especially if strong precipitation events coincide with fertilizer or pesticide application. The DFG funded project "Separating surface runoff from tile drainage flow in agricultural lowland catchments based on diatoms to improve modelled runoff components and phosphorous transport" investigates prevalent processes in this context in a 50 km² lowland catchment (Kielstau, Schleswig-Holstein, Germany) with the goal of improving existing models. End Member Mixing Analysis (EMMA) is used in the project to determine the relative importance of groundwater, tile drainage and surface runoff to streamflow at daily time steps. It became apparent that geochemical tracers are suitable for distinguishing surface runoff, but are weak for the separation of tile drainage and groundwater influence. We attribute this to the strong and complex interaction between soil water and shallow groundwater tables in the catchment. Recent studies (e.g. Pfister et al. 2011, Tauro et al. 2013) show the potential of diatoms as indicators for hydrological processes. Since we found diatoms to be suitable for the separation of tile drainage and stream samples (Wu et al., unpublished data) in our catchment, we are able to include diatom derived indices (e.g. density, species moisture indices, diversity indices) as traces in EMMA. Our results show that the inclusion of diatom data in the EMMA dataset improves the ability to distinguish tile drainage, groundwater and surface runoff influence to streamflow in our agriculturally dominated lowland catchment. Keywords: tile drainage, surface runoff, groundwater, hydrograph separation, EMMA, dia-toms, water quality, lowland catchments References: Pfister L, Wetzel CE, Martínez-Carreras N, Frentress J, Ector L, Hoffmann L, McDonnell JJ. 2011. Do diatoms run downhill? Using biodiversity of terrestrial and aquatic diatoms to identify hydrological connectivity between aquatic zones in Luxembourg. AGU Fall Meeting. Tauro F, Martínez-Carreras N, Wetzel CE, Hissler C, Barnich F, Frentress J, Ector L, Hoff-mann L, McDonnell JJ, Pfister L. 2013. Fluorescent diatoms as hydrological tracers: a proof of concept percolation experiment. EGU abstract, EGU2013-7687-4.

Towards an understanding of the molecular regulation of carbon allocation in diatoms: the interaction of energy and carbon allocation.

PubMed

Wagner, Heiko; Jakob, Torsten; Fanesi, Andrea; Wilhelm, Christian

2017-09-05

In microalgae, the photosynthesis-driven CO 2 assimilation delivers cell building blocks that are used in different biosynthetic pathways. Little is known about how the cell regulates the subsequent carbon allocation to, for example, cell growth or for storage. However, knowledge about these regulatory mechanisms is of high biotechnological and ecological importance. In diatoms, the situation becomes even more complex because, as a consequence of their secondary endosymbiotic origin, the compartmentation of the pathways for the primary metabolic routes is different from green algae. Therefore, the mechanisms to manipulate the carbon allocation pattern cannot be adopted from the green lineage. This review describes the general pathways of cellular energy distribution from light absorption towards the final allocation of carbon into macromolecules and summarizes the current knowledge of diatom-specific allocation patterns. We further describe the (limited) knowledge of regulatory mechanisms of carbon partitioning between lipids, carbohydrates and proteins in diatoms. We present solutions to overcome the problems that hinder the identification of regulatory elements of carbon metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Genetic and metabolic engineering in diatoms.

PubMed

Huang, Weichao; Daboussi, Fayza

2017-09-05

Diatoms have attracted considerable attention due to their success in diverse environmental conditions, which probably is a consequence of their complex origins. Studies of their metabolism will provide insight into their adaptation capacity and are a prerequisite for metabolic engineering. Several years of investigation have led to the development of the genome engineering tools required for such studies, and a profusion of appropriate tools is now available for exploring and exploiting the metabolism of these organisms. Diatoms are highly prized in industrial biotechnology, due to both their richness in natural lipids and carotenoids and their ability to produce recombinant proteins, of considerable value in diverse markets. This review provides an overview of recent advances in genetic engineering methods for diatoms, from the development of gene expression cassettes and gene delivery methods, to cutting-edge genome-editing technologies. It also highlights the contributions of these rapid developments to both basic and applied research: they have improved our understanding of key physiological processes; and they have made it possible to modify the natural metabolism to favour the production of specific compounds or to produce new compounds for green chemistry and pharmaceutical applications.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Multisignal control of expression of the LHCX protein family in the marine diatom Phaeodactylum tricornutum

PubMed Central

Taddei, Lucilla; Stella, Giulio Rocco; Rogato, Alessandra; Bailleul, Benjamin; Fortunato, Antonio Emidio; Annunziata, Rossella; Sanges, Remo; Thaler, Michael; Lepetit, Bernard; Lavaud, Johann; Jaubert, Marianne; Finazzi, Giovanni; Bouly, Jean-Pierre; Falciatore, Angela

2016-01-01

Diatoms are phytoplanktonic organisms that grow successfully in the ocean where light conditions are highly variable. Studies of the molecular mechanisms of light acclimation in the marine diatom Phaeodactylum tricornutum show that carotenoid de-epoxidation enzymes and LHCX1, a member of the light-harvesting protein family, both contribute to dissipate excess light energy through non-photochemical quenching (NPQ). In this study, we investigate the role of the other members of the LHCX family in diatom stress responses. Our analysis of available genomic data shows that the presence of multiple LHCX genes is a conserved feature of diatom species living in different ecological niches. Moreover, an analysis of the levels of four P. tricornutum LHCX transcripts in relation to protein expression and photosynthetic activity indicates that LHCXs are differentially regulated under different light intensities and nutrient starvation, mostly modulating NPQ capacity. We conclude that multiple abiotic stress signals converge to regulate the LHCX content of cells, providing a way to fine-tune light harvesting and photoprotection. Moreover, our data indicate that the expansion of the LHCX gene family reflects functional diversification of its members which could benefit cells responding to highly variable ocean environments. PMID:27225826

The Effects of Climate Variability on Phytoplankton Composition in the Equatorial Pacific Ocean using a Model and a Satellite-Derived Approach

NASA Technical Reports Server (NTRS)

Rousseaux, C. S.; Gregg, W. W.

2012-01-01

Compared the interannual variation in diatoms, cyanobacteria, coccolithophores and chlorophytes from the NASA Ocean Biogeochemical Model with those derived from satellite data (Hirata et al. 2011) between 1998 and 2006 in the Equatorial Pacific. Using NOBM, La Ni a events were characterized by an increase in diatoms (correlation with MEI, r=-0.81, P<0.05), while cyanobacteria concentrations decreased significantly (r=0.61; P<0.05). El Nino produced the reverse pattern, with cyanobacteria populations increasing while diatoms plummeted. This represented a radical shift in the phytoplankton community in response to climate variability. However, satellite-derived phytoplankton groups were all negatively correlated with climate variability (r ranged from -0.39 for diatoms to -0.64 for coccolithophores, P<0.05). Spatially, the satellite-derived approach was closer to an independent in situ dataset for all phytoplankton groups except diatoms than NOBM. However, the different responses of phytoplankton to intense interannual events in the Equatorial Pacific raises questions about the representation of phytoplankton dynamics in models and algorithms: is a phytoplankton community shift as in the model or an across-the-board change in abundances of all phytoplankton as in the satellite-derived approach.

Identifying metabolic pathways for production of extracellular polymeric substances by the diatom Fragilariopsis cylindrus inhabiting sea ice.

PubMed

Aslam, Shazia N; Strauss, Jan; Thomas, David N; Mock, Thomas; Underwood, Graham J C

2018-05-01

Diatoms are significant primary producers in sea ice, an ephemeral habitat with steep vertical gradients of temperature and salinity characterizing the ice matrix environment. To cope with the variable and challenging conditions, sea ice diatoms produce polysaccharide-rich extracellular polymeric substances (EPS) that play important roles in adhesion, cell protection, ligand binding and as organic carbon sources. Significant differences in EPS concentrations and chemical composition corresponding to temperature and salinity gradients were present in sea ice from the Weddell Sea and Eastern Antarctic regions of the Southern Ocean. To reconstruct the first metabolic pathway for EPS production in diatoms, we exposed Fragilariopsis cylindrus, a key bi-polar diatom species, to simulated sea ice formation. Transcriptome profiling under varying conditions of EPS production identified a significant number of genes and divergent alleles. Their complex differential expression patterns under simulated sea ice formation was aligned with physiological and biochemical properties of the cells, and with field measurements of sea ice EPS characteristics. Thus, the molecular complexity of the EPS pathway suggests metabolic plasticity in F. cylindrus is required to cope with the challenging conditions of the highly variable and extreme sea ice habitat.

Intrinsic photoluminescence of diatom shells in sensing applications

NASA Astrophysics Data System (ADS)

De Tommasi, E.; Rendina, I.; Rea, I.; De Stefano, M.; Lamberti, A.; De Stefano, L.

2009-05-01

Diatoms are monocellular micro-algae provided with external valves, the frustules, made of amorphous hydrated silica. Frustules present patterns of regular arrays of holes, the areolae, characterized by sub-micrometric dimensions. Frustules from centric diatoms are characterized by a radial disposition of areolae and exhibit several optical properties, such as photoluminescence, lens-like behavior and, in general, photonic-crystal-like behavior as long as confinement of electromagnetic field is concerned. In particular, intrinsic photoluminescence from frustules is strongly influenced by the surrounding atmosphere: on exposure to gases, the induced luminescence changes both in the optical intensity and peaks positions. To give specificity against a target analyte, a key feature for an optical sensor, a biomolecular probe, which naturally recognizes its ligand, can be covalently linked to the diatom surface. We explored the photoluminescence emission properties of frustules of Coscinodiscus wailesii centric species, characterized by a diameter of about 100-200 μm, on exposure to different vapours and in presence of specific bioprobes interacting with target analytes. Very high sensitivities have been observed due to the characteristic morphology of diatoms shells. Particular attention has been devoted to the emission properties of single frustules.

Accumulation of petroleum hydrocarbons in intracellular lipid bodies of the freshwater diatom Synedra acus subsp. radians.

PubMed

Shishlyannikov, Sergey M; Nikonova, Alyona A; Klimenkov, Igor V; Gorshkov, Alexander G

2017-01-01

The accumulation of hydrophobic compounds by phytoplankton plays a crucial role in the biogeochemical cycle of persistent organic pollutants (POPs) in aquatic environments. We studied the accumulation of polycyclic aromatic hydrocarbons (PAHs) in the freshwater diatom Synedra acus subsp. radians during its cultivation with crude oil hydrocarbons, using epifluorescent and laser confocal microscopy as well as gas chromatography-mass spectrometry (GC/MS) analysis. Our results revealed that in the presence of crude oil or an extract of a crude oil/n-hexane solution (light oil), S. acus subsp. radians accumulated PAHs in its lipid bodies. During cultivation in the presence of a crude oil/n-hexane solution, the cells selectively accumulated C12-C18 alkanes, with a preference for C15 and C16 homologues. The length of n-alkane hydrocarbon chains accumulated in cells was similar to the acyl chains of fatty acids of the diatom. We therefore suggest that the insertion of n-alkanes into the membrane lipid bilayer promotes the transmembrane transport of PAH in diatoms. Our results confirm the hypothesis that diatoms play a role in the elimination of hydrophobic hydrocarbons from aquatic systems.

Identifying community thresholds for lotic benthic diatoms in response to human disturbance.

PubMed

Tang, Tao; Tang, Ting; Tan, Lu; Gu, Yuan; Jiang, Wanxiang; Cai, Qinghua

2017-06-23

Although human disturbance indirectly influences lotic assemblages through modifying physical and chemical conditions, identifying thresholds of human disturbance would provide direct evidence for preventing anthropogenic degradation of biological conditions. In the present study, we used data obtained from tributaries of the Three Gorges Reservoir in China to detect effects of human disturbance on streams and to identify disturbance thresholds for benthic diatoms. Diatom species composition was significantly affected by three in-stream stressors including TP, TN and pH. Diatoms were also influenced by watershed % farmland and natural environmental variables. Considering three in-stream stressors, TP was positively influenced by % farmland and % impervious surface area (ISA). In contrast, TN and pH were principally affected by natural environmental variables. Among measured natural environmental variables, average annual air temperature, average annual precipitation, and topsoil % CaCO 3 , % gravel, and total exchangeable bases had significant effects on study streams. When effects of natural variables were accounted for, substantial compositional changes in diatoms occurred when farmland or ISA land use exceeded 25% or 0.3%, respectively. Our study demonstrated the rationale for identifying thresholds of human disturbance for lotic assemblages and addressed the importance of accounting for effects of natural factors for accurate disturbance thresholds.

Solar UV exposures measured simultaneously to all arbitrarily oriented leaves on a plant.

PubMed

Parisi, Alfio V; Schouten, Peter; Downs, Nathan J; Turner, Joanna

2010-05-03

The possible ramifications of climate change include the influence it has upon the amount of cloud cover in the atmosphere. Clouds cause significant variation in the solar UV radiation reaching the earth's surface and in turn the amount incident on ecosystems. The consequences of changes in solar UV radiation delivered to ecosystems due to climate change may be significant and should be investigated. Plants are an integral part of the world wide ecological balance, and research has shown they are affected by variations in solar UV radiation. Therefore research into the influence of solar UV radiation on plants is of particular significance. However, this requires a means of obtaining detailed information on the solar UV radiation received by plants. This research describes a newly developed dosimetric technique employed to gather information on solar UV radiation incident to the leaves of plants in combination with the measurement of spectral irradiances in order to provide an accurate method of collecting detailed information on the solar UV radiation affecting the canopy and lower leaf layers of individual plants. Variations in the measurements take into account the inclination and orientation of each leaf investigated, as well as the influence of shading by other leaves in the plant canopy. Copyright 2010 Elsevier B.V. All rights reserved.

Surface-water quality, Oneida Reservation and vicinity, Wisconsin, 1997-98

USGS Publications Warehouse

Schmidt, Morgan A.; Scudder, Barbara C.; Richards, Kevin D.

2000-01-01

Assessments of the benthic algal community provided relative results as did invertebrate community assessments. Shannon-Wiener diversity values for diatoms indicate that algal communities are under minor stress in four of five streams sampled and under moderate stress in Dutchman Creek. A pollution index based on the percentages of diatoms that are pollution sensitive and pollution tolerant revealed that pollution at Dutchman Creek likely is moderate; pollution at the other four sampled creeks is either minor or nonexistent in terms of effects on the diatom community.

Freshwater diatomite deposits in the western United States

USGS Publications Warehouse

Wallace, Alan R.; Frank, David G.; Founie, Alan

2006-01-01

Freshwater diatomite deposits in the Western United States are found in lake beds that formed millions of years ago. These diatom-rich sediments are among the Nation's largest commercial diatomite deposits. Each deposit contains billions of tiny diatom skeletons, which are widely used for filtration, absorption, and abrasives. New studies by the U.S. Geological Survey (USGS) are revealing how ancient lakes in the Western States produced such large numbers of diatoms. These findings can be used by both land-use managers and mining companies to better evaluate diatomite resources in the region.

Evaluation of hydrogen as a cryogenic wind tunnel test gas

NASA Technical Reports Server (NTRS)

Haut, R. C.

1977-01-01

The nondimensional ratios used to describe various flow situations in hydrogen were determined and compared with the corresponding ideal diatomic gas ratios. The results were used to examine different inviscid flow configurations. The relatively high value of the characteristic rotational temperature causes the behavior of hydrogen, under cryogenic conditions, to deviate substantially from the behavior of an ideal diatomic gas in the compressible flow regime. Therefore, if an idea diatomic gas is to be modeled, cryogenic hydrogen is unacceptable as a wind tunnel test gas in a compressible flow situation.

Late Holocene environmental changes in a mesotidal estuary from Patagonia, Argentina

NASA Astrophysics Data System (ADS)

Espinosa, Marcela; Escandell, Alejandra; Velez Agudelo, Camilo

2016-04-01

Two sediment records from the lower valley of Negro River, Patagonia, Argentina (41°01´S; 62°47'W) spanning for the last 2000 cal yrs BP were analyzed according to diatoms and sediments contents. The river originates at the junction of the Neuquén and the Limay Rivers, Northern Patagonia, and discharges more than 1000 m3/s to the South Atlantic Ocean. Mesotidal conditions dominate at the inlet (2.95 m) affecting the lower valley (about 20 km) where salinity decreases drastically in the last 2 km. Fossil diatom assemblages and grain size were studied from two cores located at 1.5 km (Villarino site) and 12 km (Criadero site) from the inlet. Samples for modern diatom analyses were collected from the littoral zone at eleven sites along the river. Physical and chemical variables were quantified representing the maximum heterogeneity along the aquatic environment. Turbidity, salinity, conductivity, pH and temperature data were obtained in situ during summer and winter. In addition, a surface sediment sample was taken for grain size analysis and organic matter content, and water samples were taken to analyze nutrients and major ions following standard methods. The diatom content of modern sediment samples were studied in order to achieve ecological information useful as modern analogous for Patagonian rivers. Diatom zones were characterized by constrained incremental sum of squares cluster analysis (single linkage, Euclidean distance) in the fossil sequences. Fossil and modern diatom assemblages were compared with Detrended Correspondence Analysis (DCA). A total of 77 samples (modern and fossils) were analyzed and more than 200 taxa were identified. Diatom assemblages showed distinct abundance patterns in relation to salinity with a shift from communities dominated by marine/brackish taxa in lower sites to communities dominated by freshwater taxa in the middle and upper course of the river. The record of Criadero core (12 km from the inlet) began 2000 cal yrs BP with a shallow vegetated brackish/freshwater environment represented by Surirella brebissonii, Epithemia adnata and Rhopalodia gibba. The environment evolved gradually into marine conditions with dominance of Paralia sulcata, Delphineis surirella, Raphoneis amphiceros and Cymatosira belgica (tidal channel). Finally, marine brackish aerophilous taxa indicate the development of a saltmarsh. Villarino core (1.5 km from the inlet) represents the infilling of the estuary during the last 1300 cal yrs BP with the dominance of the marine/brackish tychoplankton taxa Paralia sulcata. The fossil assemblages of the two studied sequences showed similarity with modern assemblages of the lower valley of the river. Considering the strong influence of salinity changes on diatom assemblages, tidal effects are the main controlling factor for the composition and distribution of diatoms along mesotidal estuaries from Patagonia. The knowledge of palaeoenvironmental conditions derived from fossil diatom assemblages is very important to infer man-made changes in coastal areas and can be used as reference for the assessment of recent coastal changes (dredging, harbour construction, flood control improvements, pollution).

Beam-plasma dielectric tensor with Mathematica

NASA Astrophysics Data System (ADS)

Bret, A.

2007-03-01

We present a Mathematica notebook allowing for the symbolic calculation of the 3×3 dielectric tensor of an electron-beam plasma system in the fluid approximation. Calculation is detailed for a cold relativistic electron beam entering a cold magnetized plasma, and for arbitrarily oriented wave vectors. We show how one can elaborate on this example to account for temperatures, arbitrarily oriented magnetic field or a different kind of plasma. Program summaryTitle of program: Tensor Catalog identifier: ADYT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYT_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers: Any computer running Mathematica 4.1. Tested on DELL Dimension 5100 and IBM ThinkPad T42. Installations: ETSI Industriales, Universidad Castilla la Mancha, Ciudad Real, Spain Operating system under which the program has been tested: Windows XP Pro Programming language used: Mathematica 4.1 Memory required to execute with typical data: 7.17 Mbytes No. of bytes in distributed program, including test data, etc.: 33 439 No. of lines in distributed program, including test data, etc.: 3169 Distribution format: tar.gz Nature of the physical problem: The dielectric tensor of a relativistic beam plasma system may be quite involved to calculate symbolically when considering a magnetized plasma, kinetic pressure, collisions between species, and so on. The present Mathematica notebook performs the symbolic computation in terms of some usual dimensionless variables. Method of solution: The linearized relativistic fluid equations are directly entered and solved by Mathematica to express the first-order expression of the current. This expression is then introduced into a combination of Faraday and Ampère-Maxwell's equations to give the dielectric tensor. Some additional manipulations are needed to express the result in terms of the dimensionless variables. Restrictions on the complexity of the problem: Temperature effects are limited to small, i.e. non-relativistic, temperatures. The kinetic counterpart of the present Mathematica will usually not compute the required integrals. Typical running time: About 1 minute on a Intel Centrino 1.5 GHz Laptop with 512 MB of RAM. Unusual features of the program: None.

Comparison of potential diatom 'barcode' genes (the 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta.

PubMed

Guo, Liliang; Sui, Zhenghong; Zhang, Shu; Ren, Yuanyuan; Liu, Yuan

2015-04-01

Diatoms form an enormous group of photoautotrophic micro-eukaryotes and play a crucial role in marine ecology. In this study, we evaluated typical genes to determine whether they were effective at different levels of diatom clustering analysis to assess the potential of these regions for barcoding taxa. Our test genes included nuclear rRNA genes (the nuclear small-subunit rRNA gene and the 5.8S rRNA gene+ITS-2), a mitochondrial gene (cytochrome c-oxidase subunit 1, COI), a chloroplast gene [ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (rbcL)] and the universal plastid amplicon (UPA). Calculated genetic divergence was highest for the internal transcribed spacer (ITS; 5.8S+ITS-2) (p-distance of 1.569, 85.84% parsimony-informative sites) and COI (6.084, 82.14%), followed by the 18S rRNA gene (0.139, 57.69%), rbcL (0.120, 42.01%) and UPA (0.050, 14.97%), which indicated that ITS and COI were highly divergent compared with the other tested genes, and that their nucleotide compositions were variable within the whole group of diatoms. Bayesian inference (BI) analysis showed that the phylogenetic trees generated from each gene clustered diatoms at different phylogenetic levels. The 18S rRNA gene was better than the other genes in clustering higher diatom taxa, and both the 18S rRNA gene and rbcL performed well in clustering some lower taxa. The COI region was able to barcode species of some genera within the Bacillariophyceae. ITS was a potential marker for DNA based-taxonomy and DNA barcoding of Thalassiosirales, while species of Cyclotella, Skeletonema and Stephanodiscus gathered in separate clades, and were paraphyletic with those of Thalassiosira. Finally, UPA was too conserved to serve as a diatom barcode. © 2015 IUMS.

Toxicity of dissolved and precipitated aluminium to marine diatoms.

PubMed

Gillmore, Megan L; Golding, Lisa A; Angel, Brad M; Adams, Merrin S; Jolley, Dianne F

2016-05-01

Localised aluminium contamination can lead to high concentrations in coastal waters, which have the potential for adverse effects on aquatic organisms. This research investigated the toxicity of 72-h exposures of aluminium to three marine diatoms (Ceratoneis closterium (formerly Nitzschia closterium), Minutocellus polymorphus and Phaeodactylum tricornutum) by measuring population growth rate inhibition and cell membrane damage (SYTOX Green) as endpoints. Toxicity was correlated to the time-averaged concentrations of different aluminium size-fractions, operationally defined as <0.025μm filtered, <0.45μm filtered (dissolved) and unfiltered (total) present in solution over the 72-h bioassay. The chronic population growth rate inhibition after aluminium exposure varied between diatom species. C. closterium was the most sensitive species (10% inhibition of growth rate (72-h IC10) of 80 (55-100)μg Al/L (95% confidence limits)) while M. polymorphus (540 (460-600)μg Al/L) and P. tricornutum (2100 (2000-2200)μg Al/L) were less sensitive (based on measured total aluminium). Dissolved aluminium was the primary contributor to toxicity in C. closterium, while a combination of dissolved and precipitated aluminium forms contributed to toxicity in M. polymorphus. In contrast, aluminium toxicity to the most tolerant diatom P. tricornutum was due predominantly to precipitated aluminium. Preliminary investigations revealed the sensitivity of C. closterium and M. polymorphus to aluminium was influenced by initial cell density with aluminium toxicity significantly (p<0.05) increasing with initial cell density from 10(3) to 10(5)cells/mL. No effects on plasma membrane permeability were observed for any of the three diatoms suggesting that mechanisms of aluminium toxicity to diatoms do not involve compromising the plasma membrane. These results indicate that marine diatoms have a broad range in sensitivity to aluminium with toxic mechanisms related to both dissolved and precipitated aluminium. Copyright © 2016 Elsevier B.V. All rights reserved.

Tinted windows: The presence of the UV absorbing compounds called mycosporine-like amino acids embedded in the frustules of marine diatoms

NASA Astrophysics Data System (ADS)

Ingalls, Anitra E.; Whitehead, Kenia; Bridoux, Maxime C.

2010-01-01

Diatom frustule-bound organic compounds presumably play an important role in biomineralization and constitute an important pool of organic matter preserved in diatom frustule-rich sediments. In this study, detailed analysis of diatom frustule-bound organic matter in opal-rich Southern Ocean plankton and sediments revealed for the first time the presence of low molecular weight, UV light absorbing compounds called mycosporine-like amino acids (MAAs). Chemically cleaned diatom frustule-derived biosilica was dissolved in HF, releasing bound or entrapped organic compounds that were subsequently characterized using liquid chromatography with UV-Vis and electrospray ionization mass spectrometry (LC/PDA/ESI-MS). Palythine ([M+H] + = 245), porphyra-334 ([M+H] + = 347) and shinorine ([M+H] + = 333) were the most abundant MAAs detected in HF digests of plankton and sediment. Traces of asterina ([M+H] + = 289), palythinol ([M+H] + = 303) and palythinic acid ([M+H] + = 329) were also detected. MAAs in cleaned HF digested frustules were up to two orders of magnitude more abundant than methanol extractable MAAs. MAAs are substituted with acid hydrolysable amino acid residues. Our results suggest that MAAs, and not proteins, could be responsible for the high proportion of the amino acids glycine and threonine found in hydrolysates of HF digested diatom-rich environmental samples. Total MAAs accounted for 3-27% of the carbon and 2-18% of total nitrogen in the frustules undergoing various chemical cleaning treatments. This is the first report of MAAs in close association with a mineral phase and we hypothesize that the mineral matrix could stabilize these compounds, thereby enhancing photoprotection against the harmful effects of UV light. The presence of frustule-bound MAAs in sediment cores further suggests the possibility that they could be used in compound-specific isotope analysis of diatom-bound organic matter and as indicators of past solar irradiance.

Reproduction of Pseudocalanus newmani (Copepoda: Calanoida) is deleteriously affected by diatom blooms A field study

NASA Astrophysics Data System (ADS)

Halsband-Lenk, Claudia; Pierson, James J.; Leising, Andrew W.

2005-11-01

Copepod secondary production has traditionally been linked to the spring diatom bloom in temperate and high latitudes, but laboratory studies have recently challenged this view and have shown either reduced fecundity or viability of offspring when copepods were fed high concentrations of - mostly unialgal - diatoms. However, field evidence that diatoms affect copepod reproduction is still scarce. We analyzed the reproductive response of a common, small calanoid copepod of the boreal Pacific, Pseudocalanus newmani, to spring diatom blooms in Dabob Bay, a semi-enclosed fjord of Puget Sound, Washington, USA. Abundance patterns, egg production rates, egg hatching success, and naupliar viability of the egg-carrying copepod were examined between February and early May in the years 2002-2004. The population underwent strong variations in abundance during both years, with high abundance of all stages from February to mid-March, but dramatically decreasing individual numbers later in spring. A recovery to higher numbers occurred in July. While egg production rates were independent of chlorophyll concentrations, the reproductive success of P. newmani was negatively affected by certain phytoplankton bloom conditions. Hatching success and - more markedly - naupliar survival were reduced following peaks of Thalassiosira species that were producing anti-mitotic aldehydes, but were high during periods when phytoplankton blooms were more diverse or dominated by other prey taxa including diatoms. As a consequence, recruitment of the naupliar population was considerably affected by the Thalassiosira blooms. This study shows for the first time that the so-called diatom effect operates in nature when all prerequisites - (1) high concentration of aldehyde producers, (2) few prey alternatives, and (3) feeding of copepods on these algae - are given. However, the effect was transient in Dabob Bay and may be so in other pelagic ecosystems. It remains to discern the potential sources of mortality, such as toxicity, malnutrition, predation, and/or advection, that may have caused the strong decline of the Pseudocalanus population during April.

Multiple nitrogen isotope recorders for surface ocean nitrate utilization in the Subarctic North Pacific and the Bering Sea

NASA Astrophysics Data System (ADS)

Ren, H. A.; Anderson, R.; Sigman, D. M.; Studer, A.; Winckler, G.; Haugh, G.; Serno, S.; Gersonde, R.

2017-12-01

Sedimentary nitrogen isotopes have been developed as a proxy to reconstruct the degree of nitrate utilization in the polar surface oceans. But its application could be compromised by 1) uncertainties on the biological production, transport, and preservation of the organic material in the sediments, and 2) potential changes in the isotopic composition of the nitrate source, that is remotely controlled by processes in other regions. In this study, we map and compare spatial patterns of three d15N recorders (bulk sedimentary nitrogen, the organic nitrogen within cleaned diatom frustules or diatom-bound N, and within planktonic foraminifera tests or foraminifera-bound N) from multicore surface sediments across the Subarctic North Pacific (SNP) and the Bering Sea between 60°N and 35°N. Diatom-bound d15N varies between 3.5 and 8.5‰. Its spatial variation is reversely correlated with changes in the surface nitrate concentration, and is consistent with the expected d15N change of the export production in a simple nitrate assimilation model. Similar to previous findings, diatom-bound d15N is generally 2 4‰ higher than the modeled d15N value of the export production, likely reflecting a biomass to frustual-bound N difference. However, the greater d15N elevation observed in the eastern open SNP may be best explained by lateral transport of residual surface nitrate enriched in 15N from the western SNP. The d15N of Neogloboquadrina pachyderma (sinistral) is similar to the diatom-bound d15N within 1‰. Bulk sedimentary d15N generally agrees with diatom-bound d15N, but is more variable. It is higher than diatom-bound d15N in the eastern and western transect close to the shelf area, likely reflecting a terrigenous source, while exceptionally low d15N values were found on the Bering Sea shelf, possibly due to contamination by mineral-associated inorganic N.

Characterization of Putative Iron Responsive Genes as Species-Specific Indicators of Iron Stress in Thalassiosiroid Diatoms

PubMed Central

Whitney, LeAnn P.; Lins, Jeremy J.; Hughes, Margaret P.; Wells, Mark L.; Chappell, P. Dreux; Jenkins, Bethany D.

2011-01-01

Iron (Fe) availability restricts diatom growth and primary production in large areas of the oceans. It is a challenge to assess the bulk Fe nutritional health of natural diatom populations, since species can differ in their physiological and molecular responses to Fe limitation. We assayed expression of selected genes in diatoms from the Thalassiosira genus to assess their potential utility as species-specific molecular markers to indicate Fe status in natural diatom assemblages. In this study, we compared the expression of the photosynthetic genes encoding ferredoxin (a Fe-requiring protein) and flavodoxin (a Fe-free protein) in culture experiments with Fe replete and Fe stressed Thalassiosira pseudonana (CCMP 1335) isolated from coastal waters and Thalassiosira weissflogii (CCMP 1010) isolated from the open ocean. In T. pseudonana, expression of flavodoxin and ferredoxin genes were not sensitive to Fe status but were found to display diel periodicities. In T. weissflogii, expression of flavodoxin was highly responsive to iron levels and was only detectable when cultures were Fe limited. Flavodoxin genes have been duplicated in most diatoms with available genome data and we show that T. pseudonana has lost its copy related to the Fe-responsive copy in T. weissflogii. We also examined the expression of genes for a putative high affinity, copper (Cu)-dependent Fe uptake system in T. pseudonana. Our results indicate that genes encoding putative Cu transporters, a multi-Cu oxidase, and a Fe reductase are not linked to Fe status. The expression of a second putative Fe reductase increased in Fe limited cultures, but this gene was also highly expressed in Fe replete cultures, indicating it may not be a useful marker in the field. Our findings highlight that Fe metabolism may differ among diatoms even within a genus and show a need to validate responses in different species as part of the development pipeline for genetic markers of Fe status in field populations. PMID:22275908

New species of Eunotia from small isolated wetlands in Florida

EPA Science Inventory

Diatom species composition of small wetlands is diverse and unique due to a plethora of spatial and temporal variables. Diatoms from small wetlands can contribute greatly to better understanding microbial biodiversity, distribution, dispersal and populations.

Diatom-templated TiO2 with enhanced photocatalytic activity: biomimetics of photonic crystals

NASA Astrophysics Data System (ADS)

He, Jiao; Chen, Daomei; Li, Yongli; Shao, Junlong; Xie, Jiao; Sun, Yuejuan; Yan, Zhiying; Wang, Jiaqiang

2013-11-01

The siliceous frustules with sophisticated optical structure endow diatoms with superior solar light-harvesting abilities for effective photosynthesis. The preserved frustules of diatom ( Cocconeis placentula) cells, as biophotonic crystals, were thus employed as both hard templates and silicon resources to synthesize TiO2 photocatalyst. Characterizations by a combination of physicochemical techniques proved that the bio-inspired sample is TiO2-coated SiO2 with biogenic C self-doped in. It was found that the synthesized composites exhibited similar morphologies to the original diatom templates. In comparison with commercial Degussa P25 TiO2, the C-doped TiO2/SiO2 catalyst exhibited more light absorption in the visible region and higher photocatalytic efficiency for photodegradation of rhodamine B under visible light due to the biomorphic hierarchical structures, TiO2 coating and C-doping.

Combined production of fucoxanthin and EPA from two diatom strains Phaeodactylum tricornutum and Cylindrotheca fusiformis cultures.

PubMed

Wang, Hui; Zhang, Yan; Chen, Lin; Cheng, Wentao; Liu, Tianzhong

2018-04-04

Fucoxanthin and eicosapentaenoic acid (EPA) provide significant health benefits for human population. Diatom is a potential natural livestock for the combined production of EPA and fucoxanthin. In this study, first, the effects of three important parameters including light intensity, nitrogen concentration and salinity were evaluated for the production of EPA and fucoxanthin in two diatom strains Phaeodactylum tricornutum and Cylindrotheca fusiformis. And then, two steps method based on light intensity were applied to produce EPA and fucoxanthin in large scale. Higher light intensity was first adopted for the high growth rate and lipid content of diatom, and after a period of time, light intensity was lowered to enhance the accumulation of fucoxanthin and EPA. In final, the highest EPA yields were 62.55 and 27.32 mg L -1 for P. tricornutum and C. fusiformis, and the fucoxanthin yield reached 8.32 and 6.05 mg L -1 , respectively.

Designer diatom episomes delivered by bacterial conjugation

DOE PAGES

Karas, Bogumil J.; Diner, Rachel E.; Lefebvre, Stephane C.; ...

2015-04-21

Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify amore » yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research.« less

Diatoms: a biotemplating approach to fabricating drug delivery reservoirs.

PubMed

Chao, Joshua T; Biggs, Manus J P; Pandit, Abhay S

2014-11-01

Biotemplating is a rapidly expanding subfield that utilizes nature-inspired systems and structures to create novel functional materials, and it is through these methods that the limitations of current engineering practices may be advanced. The diatom is an exceptional template for drug delivery applications, owing largely to its highly-ordered pores, large surface area, species-specific architecture, and flexibility for surface modifications. Diatoms have been studied in a wide range of biomedical applications and their potential as the next frontier of drug delivery has yet to be fully exploited. In this editorial, the authors aim to review the use of diatoms in the delivery of poorly water-soluble drugs as reported in the literature, discuss the progress and advancements that have been made thus far, identify the shortcomings and limitations in the field, and, lastly, present their expert opinion and convey the future outlook on biotemplating approaches for drug delivery.

Designer diatom episomes delivered by bacterial conjugation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karas, Bogumil J.; Diner, Rachel E.; Lefebvre, Stephane C.

Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify amore » yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research.« less

Late Pliocene diatoms in a diatomite from Prydz Bay, East Antarctica

USGS Publications Warehouse

Mahood, A.D.; Barron, J.A.

1996-01-01

Very well-preserved Pliocene diatoms from a diatomite unit interbedded within glacial sediments at Ocean Drilling Program Site 742 in Prydz Bay, Antarctica are documented and illustrated. The presence of Thalassiosira kolbei, T. torokina, Actinocyclus actinochilus, A. karstenii and the absence of Nitzschia interfrigidaria. T. insigna and T. vulnifica in Sample 119-742A-15R-4, 44-46cm constrain its age to ca. 2.2-1.8 Ma (late Pliocene). Diatoms associated with sea ice constitute 35% of the Pliocene diatom assemblage, compared with 71% of the modern sediment assemblage at the site, suggesting that sea ice was present during the late Pliocene period of deposition of the sample, although it probably was not the significant feature it is today. Thalassiosira ellitipora (Donahue) Fenner is described and illustrated in detail and is validly published. An expanded description and numerous illustrations are also presented for T. torokina Brady.

Long-term decomposition of DOC from experimental diatom blooms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fry, B.; Hopkinson, C.S. Jr.; Nolin, A.

1996-09-01

Decomposition of {sup 13}C-labeled dissolved organic carbon (DOC) produced in two marine diatom blooms was followed for 2.5 yr with large volume (20 liter) incubations performed in the dark. The {sup 13}C tracer was used to partition decomposition dynamics of the fresh diatom-derived DOC and the turnover of background DOC from Woods Hole Harbor. DOC from Woods Hole harbor proved largely refractory, with DOC concentrations falling from 122 to {approximately} 100 {mu}M C in 2.5 yr. DOC from the diatom blooms was more labile, but was also incompletely mineralized, with 25-35% remaining after 2.5 yr. Neither nutrients nor labile carbonmore » (dextrose) added at 1.5 yr significantly stimulated DOC mineralization. The experiments indicate that DOC produced in short-term blooms can be surprisingly resistant to microbial attack. 21 refs., 1 fig., 1 tab.« less

A Sequential Chemical Extraction and Spectroscopic Assessment of the Potential Bioavailability of Mercury Released From the Inoperative New Idria Mercury Mine, San Benito Co., CA

NASA Astrophysics Data System (ADS)

Jew, A. D.; Luong, P. N.; Rytuba, J. J.; Brown, G. E.

2012-12-01

The inoperative New Idria mercury mine in San Benito Co., CA, is a potential point source of Hg to the Central Valley of California. To determine the phases and the potential bioavailability of Hg present in stream bed deposits downstream of the mine, sequential chemical extractions (SCEs) targeting Hg-bearing phases and synchrotron-based spectroscopic and imaging techniques were used on sediment samples taken from the acid mine drainage (AMD) system, Hg sorbed in the laboratory to ferrihydrite (synthetic 2-line and natural), and Hg associated with diatom-rich samples. In all field samples examined, both the wet and dry seasons, removal of > 97% of the Hg required 1M KOH or harsher chemical treatments. X-ray absorption spectroscopy (XAS) showed that HgS was the dominant inorganic Hg phase present, with no detectable Hg associated with the ferrihydrite. Uptake and subsequent SCE analysis of Hg to both synthetic and natural ferrihydrite showed that 1M MgCl2 removed ≥ 90% of the total Hg, suggesting that Hg does not sorb strongly to ferrihydrite. This finding is surprising, because in most settings ferrihydrite is considered to be a strong adsorbent of heavy metals. Due to the lack of Hg sorption to ferrihydrite in field samples, another pool for the non-HgS/HgSe fraction in sediments is needed. SEM analysis of the downstream samples showed that regardless of pH, freshwater diatoms were present. To determine if diatoms were the sink for dissolved Hg in this system, SCE analysis on commercially available and diatom-rich field samples from the New Idria site and Harley Gulch (Lake County, CA) were completed. The vast majority of Hg in diatom-rich samples was removed by 1M KOH, which corresponds to the non-HgS/HgSe fraction of the New Idria field samples. Analysis for carbon and nitrogen in the diatom-rich samples showed no detectable nitrogen, indicating little to no organic material was left in the samples. We therefore infer that Hg in the diatoms is contained in the silica tests. The possibility of Hg being incorporated in the silica tests of diatoms is surprising, but one of the few known Hg-silicates (Edgarbailyite) was first discovered in the New Idria forming under ambient conditions, thus, a Hg-silicate species is possible. The stability of Hg contained in diatoms is important because it represents a new sink for dissolved Hg in an impacted system that was previously unknown. Freshwater diatoms present in the New Idria drainage system were found to contain significant quantities (30-60%) of Hg in the non-HgS SCE fractions, similar to the New Idria sediments, and are thought to be the major association of Hg in this system. SCE analyses of Hg(II) sorbed to synthetic 2-line and natural ferrihydrite in the laboratory showed that Hg(II) does not bind strongly to either material. The adsorption/incorporation of Hg(II) with the silica tests of diatoms is an important discovery and has major implications for passive remediation strategies for Hg in natural systems. Because the vast majority of Hg contained in sediments downstream of the New Idria site require 1M KOH or harsher chemical treatment for removal, the Hg released from New Idria can be considered to be environmentally stable.

Decadal-Scale Changes of Dinoflagellates and Diatoms in the Anomalous Baltic Sea Spring Bloom

PubMed Central

Klais, Riina; Tamminen, Timo; Kremp, Anke; Spilling, Kristian; Olli, Kalle

2011-01-01

The algal spring bloom in the Baltic Sea represents an anomaly from the winter-spring bloom patterns worldwide in terms of frequent and recurring dominance of dinoflagellates over diatoms. Analysis of approximately 3500 spring bloom samples from the Baltic Sea monitoring programs revealed (i) that within the major basins the proportion of dinoflagellates varied from 0.1 (Kattegat) to >0.8 (central Baltic Proper), and (ii) substantial shifts (e.g. from 0.2 to 0.6 in the Gulf of Finland) in the dinoflagellate proportion over four decades. During a recent decade (1995–2004) the proportion of dinoflagellates increased relative to diatoms mostly in the northernmost basins (Gulf of Bothnia, from 0.1 to 0.4) and in the Gulf of Finland, (0.4 to 0.6) which are typically ice-covered areas. We hypothesize that in coastal areas a specific sequence of seasonal events, involving wintertime mixing and resuspension of benthic cysts, followed by proliferation in stratified thin layers under melting ice, favors successful seeding and accumulation of dense dinoflagellate populations over diatoms. This head-start of dinoflagellates by the onset of the spring bloom is decisive for successful competition with the faster growing diatoms. Massive cyst formation and spreading of cyst beds fuel the expanding and ever larger dinoflagellate blooms in the relatively shallow coastal waters. Shifts in the dominant spring bloom algal groups can have significant effects on major elemental fluxes and functioning of the Baltic Sea ecosystem, but also in the vast shelves and estuaries at high latitudes, where ice-associated cold-water dinoflagellates successfully compete with diatoms. PMID:21747911

Decadal-scale changes of dinoflagellates and diatoms in the anomalous baltic sea spring bloom.

PubMed

Klais, Riina; Tamminen, Timo; Kremp, Anke; Spilling, Kristian; Olli, Kalle

2011-01-01

The algal spring bloom in the Baltic Sea represents an anomaly from the winter-spring bloom patterns worldwide in terms of frequent and recurring dominance of dinoflagellates over diatoms. Analysis of approximately 3500 spring bloom samples from the Baltic Sea monitoring programs revealed (i) that within the major basins the proportion of dinoflagellates varied from 0.1 (Kattegat) to >0.8 (central Baltic Proper), and (ii) substantial shifts (e.g. from 0.2 to 0.6 in the Gulf of Finland) in the dinoflagellate proportion over four decades. During a recent decade (1995-2004) the proportion of dinoflagellates increased relative to diatoms mostly in the northernmost basins (Gulf of Bothnia, from 0.1 to 0.4) and in the Gulf of Finland, (0.4 to 0.6) which are typically ice-covered areas. We hypothesize that in coastal areas a specific sequence of seasonal events, involving wintertime mixing and resuspension of benthic cysts, followed by proliferation in stratified thin layers under melting ice, favors successful seeding and accumulation of dense dinoflagellate populations over diatoms. This head-start of dinoflagellates by the onset of the spring bloom is decisive for successful competition with the faster growing diatoms. Massive cyst formation and spreading of cyst beds fuel the expanding and ever larger dinoflagellate blooms in the relatively shallow coastal waters. Shifts in the dominant spring bloom algal groups can have significant effects on major elemental fluxes and functioning of the Baltic Sea ecosystem, but also in the vast shelves and estuaries at high latitudes, where ice-associated cold-water dinoflagellates successfully compete with diatoms.

SLC4 family transporters in a marine diatom directly pump bicarbonate from seawater

PubMed Central

Nakajima, Kensuke; Tanaka, Atsuko; Matsuda, Yusuke

2013-01-01

Photosynthesis in marine diatoms is a vital fraction of global primary production empowered by CO2-concentrating mechanisms. Acquisition of HCO3− from seawater is a critical primary step of the CO2-concentrating mechanism, allowing marine photoautotrophic eukaryotes to overcome CO2 limitation in alkaline high-salinity water. However, little is known about molecular mechanisms governing this process. Here, we show the importance of a plasma membrane-type HCO3− transporter for CO2 acquisition in a marine diatom. Ten putative solute carrier (SLC) family HCO3− transporter genes were found in the genome of the marine pennate diatom Phaeodactylum tricornutum. Homologs also exist in marine centric species, Thalassiosira pseudonana, suggesting a general occurrence of SLC transporters in marine diatoms. Seven genes were found to encode putative mammalian-type SLC4 family transporters in P. tricornutum, and three of seven genes were specifically transcribed under low CO2 conditions. One of these gene products, PtSLC4-2, was localized at the plasmalemma and significantly stimulated both dissolved inorganic carbon (DIC) uptake and photosynthesis in P. tricornutum. DIC uptake by PtSLC4-2 was efficiently inhibited by an anion-exchanger inhibitor, 4,4′-diisothiocyanostilbene-2,2′-disulfonic acid, in a concentration-dependent manner and highly dependent on Na+ ions at concentrations over 100 mM. These results show that DIC influx into marine diatoms is directly driven at the plasmalemma by a specific HCO3− transporter with a significant halophilic nature. PMID:23297242

Distribution and diversity of diatom assemblages in surficial sediments of shallow lakes in Wapusk National Park (Manitoba, Canada) region of the Hudson Bay Lowlands.

PubMed

Jacques, Olivier; Bouchard, Frédéric; MacDonald, Lauren A; Hall, Roland I; Wolfe, Brent B; Pienitz, Reinhard

2016-07-01

The hydrology of shallow lakes (and ponds) located in the western Hudson Bay Lowlands (HBL) is sensitive to climate warming and associated permafrost thaw. However, their biological characteristics are poorly known, which hampers effective aquatic ecosystem monitoring. Located in northern Manitoba along the southwestern coast of Hudson Bay, Wapusk National Park (WNP) encompasses numerous shallow lakes representative of the subarctic zone. We analyzed the distribution and diversity of diatom (microscopic algae; class Bacillariophyceae) assemblages in surficial sediments of 33 lakes located in three different ecozones spanning a vegetation gradient, from NE to SW: the Coastal Fen (CF), the Interior Peat Plateau (IPP), and the Boreal Spruce Forest (BSF). We found significant differences (P < 0.05) in diatom community composition between CF and IPP lakes, and CF and BSF lakes, but not between IPP and BSF lakes. These results are consistent with water chemistry measurements, which indicated distinct limnological conditions for CF lakes. Diatom communities in CF lakes were generally dominated by alkaliphilous taxa typical of waters with medium to high conductivity, such as Nitzschia denticula. In contrast, several IPP and BSF lakes were dominated by acidophilous and circumneutral diatom taxa with preference for low conductivity (e.g., Tabellaria flocculosa, Eunotia mucophila, E. necompacta var. vixcompacta). This exploratory survey provides a first detailed inventory of the diatom assemblages in the WNP region needed for monitoring programs to detect changes in shallow lake ecosystems and ecozonal shifts in response to climate variations.

Plastid proteomics for elucidating iron limited remodeling of plastid physiology in diatoms

NASA Astrophysics Data System (ADS)

Gomes, K. M.; Nunn, B. L.; Jenkins, B. D.

2016-02-01

Diatoms are important primary producers in the world's oceans and their growth is constrained in large regions by low iron availability. This low iron-induced limitation of primary production is due to the requirement for iron in components of essential metabolic pathways including key chloroplast functions such as photosynthesis and nitrate assimilation. Diatoms can bloom and accumulate high biomass during introduction of iron into low iron waters, indicating adaptations allowing for their survival in iron-limited waters and rapid growth when iron becomes more abundant. Prior studies have shown that under iron limited stress, diatoms alter plastid-specific processes including components of electron transport, size of light harvesting capacity and chlorophyll content, suggesting plastid-specific protein regulation. Due to their complex evolutionary history, resulting from a secondary endosymbiosis, knowledge regarding the complement of plastid localized proteins remains limited in comparison to other model photosynthetic organisms. While in-silico prediction of diatom protein localization provides putative candidates for plastid-localization, these analyses can be limited as most plastid prediction models were developed using plants, primary endosymbionts. In order to characterize proteins enriched in diatom chloroplast and to understand how the plastid proteome is remodeled in response to iron limitation, we used mass spectrometry based proteomics to compare plastid- enriched protein fractions from Thalassiosira pseudonana, grown in iron replete and limited conditions. These analyses show that iron stress alters regulation of major metabolic pathways in the plastid including the Calvin cycle and fatty acid synthesis. These components provide promising targets to further characterize the plastid specific response to iron limitation.

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

DOE PAGES

Patil, Shrikant; Moeys, Sara; von Dassow, Peter; ...

2015-11-14

Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestralmore » loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. Lastly, our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.« less

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patil, Shrikant; Moeys, Sara; von Dassow, Peter

Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestralmore » loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. Lastly, our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.« less

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta.

PubMed

Patil, Shrikant; Moeys, Sara; von Dassow, Peter; Huysman, Marie J J; Mapleson, Daniel; De Veylder, Lieven; Sanges, Remo; Vyverman, Wim; Montresor, Marina; Ferrante, Maria Immacolata

2015-11-14

Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestral loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. Our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.

Detecting explosive molecules from nanoliter solution: A new paradigm of SERS sensing on hydrophilic photonic crystal biosilica.

PubMed

Kong, Xianming; Xi, Yuting; Le Duff, Paul; Chong, Xinyuan; Li, Erwen; Ren, Fanghui; Rorrer, Gregory L; Wang, Alan X

2017-02-15

We demonstrate a photonic crystal biosilica surface-enhanced Raman scattering (SERS) substrate based on a diatom frustule with in-situ synthesized silver nanoparticles (Ag NPs) to detect explosive molecules from nanoliter (nL) solution. By integrating high density Ag NPs inside the nanopores of diatom biosilica, which is not achievable by traditional self-assembly techniques, we obtained ultra-high SERS sensitivity due to dual enhancement mechanisms. First, the hybrid plasmonic-photonic crystal biosilica with three dimensional morphologies was obtained by electroless-deposited Ag seeds at nanometer sized diatom frustule surface, which provides high density hot spots as well as strongly coupled optical resonances with the photonic crystal structure of diatom frustules. Second, we discovered that the evaporation-driven microscopic flow combined with the strong hydrophilic surface of diatom frustules is capable of concentrating the analyte molecules, which offers a simple yet effective mechanism to accelerate the mass transport into the SERS substrate. Using the inkjet printing technology, we are able to deliver multiple 100pico-liter (pL) volume droplets with pinpoint accuracy into a single diatom frustule with dimension around 30µm×7µm×5µm, which allows for label-free detection of explosive molecules such as trinitrotoluene (TNT) down to 10 -10 M in concentration and 2.7×10 -15 g in mass from 120nL solution. Our research illustrates a new paradigm of SERS sensing to detect trace level of chemical compounds from minimum volume of analyte using nature created photonic crystal biosilica materials. Copyright © 2016 Elsevier B.V. All rights reserved.

Detecting explosive molecules from nanoliter solution: A new paradigm of SERS sensing on hydrophilic photonic crystal biosilica

PubMed Central

Kong, Xianming; Xi, Yuting; Le Duff, Paul; Chong, Xinyuan; Li, Erwen; Ren, Fanghui; Rorrer, Gregory L.; Wang, Alan X.

2017-01-01

We demonstrate a photonic crystal biosilica surface-enhanced Raman scattering (SERS) substrate based on a diatom frustule with in-situ synthesized silver nanoparticles (Ag NPs) to detect explosive molecules from nanoliter (nL) solution. By integrating high density Ag NPs inside the nanopores of diatom biosilica, which is not achievable by traditional self-assembly techniques, we obtained ultra-high SERS sensitivity due to dual enhancement mechanisms. First, the hybrid plasmonic-photonic crystal biosilica with three dimensional morphologies was obtained by electroless-deposited Ag seeds at nanometer sized diatom frustule surface, which provides high density hot spots as well as strongly coupled optical resonances with the photonic crystal structure of diatom frustules. Second, we discovered that the evaporation-driven microscopic flow combined with the strong hydrophilic surface of diatom frustules is capable of concentrating the analyte molecules, which offers a simple yet effective mechanism to accelerate the mass transport into the SERS substrate. Using the inkjet printing technology, we are able to deliver multiple 100 pico-liter (pL) volume droplets with pinpoint accuracy into a single diatom frustule with dimension around 30 μm × 7 μm × 5 μm, which allows for label-free detection of explosive molecules such as trinitrotoluene (TNT) down to 10−10 M in concentration and 2.7 × 10−15 g in mass from 120 nL solution. Our research illustrates a new paradigm of SERS sensing to detect trace level of chemical compounds from minimum volume of analyte using nature created photonic crystal biosilica materials. PMID:27471144

Isolation and characterization of a single-stranded RNA virus infecting the bloom-forming diatom Chaetoceros socialis.

PubMed

Tomaru, Yuji; Takao, Yoshitake; Suzuki, Hidekazu; Nagumo, Tamotsu; Nagasaki, Keizo

2009-04-01

Diatoms are very significant primary producers in the world's oceans. Various environmental factors affect the depletion of diatom populations. The importance of viruses as a potential mortality source has recently been recognized. We isolated and characterized a new diatom virus (Chaetoceros socialis f. radians RNA virus [CsfrRNAV]) causing the lysis of the bloom-forming species Chaetoceros socialis Lauder f. radians (Schütt) Proschkina-Lavrenko. The virus infectious to C. socialis f. radians was isolated from water samples collected in Hiroshima Bay. Here we show the physiology, morphology, and genome characteristics of the virus clone. Virions were 22 nm in diameter and accumulated in the cytoplasm of the host cells. The latent period and the burst size were estimated to be <48 h and 66 infectious units per host cell, respectively. CsfrRNAV harbors a single-stranded RNA (ssRNA) genome and encodes at least three polypeptides of 32.0, 28.5, and 25.0 kDa. Sequencing analysis shows the length of the genome is 9,467 bases, excluding a poly(A) tail. The monophyly of CsfrRNAV and other diatom-infecting RNA viruses, Rhizosolenia setigera RNA virus and Chaetoceros tenuissimus RNA virus, was strongly supported by phylogenetic analysis based on the amino acid sequence of the RNA-dependent RNA polymerase domains. This suggested a new ssRNA virus family, Bacillariornaviridae. This discovery of CsfrRNAV may aid in further understanding the ecological dynamics of the C. socialis f. radians population in nature and the relationships between ssRNA diatom viruses and their hosts.

Diatom Evidence for Climatic Changes Associated With the Slowdown of the Meridional Overturning Circulation in the Last 50 Years in the Mexican Tropical Pacific.

NASA Astrophysics Data System (ADS)

Machain-Castillo, M. L.; Almaraz-Ruiz, L.; Esparza-Alvarez, M. A.; Ruiz-Fernandez, A. C.; Sanchez-Cabeza, J. A.; Hernandez-Becerril, D. U.

2016-12-01

Laminated sediments from the Gulf of Tehuantepec, Mexican Tropical Pacific, reveal climatic variability during the last 50 years. The Gulf of Tehuantepec is characterized by strong upwelling during the autumn-winter season due to intense northern winds. Upwelling supplies high nutrient concentrations and cold water to the ocean surface, resulting in high biological productivity, including diatom blooms. The rest of the year winds are relatively calm and currents predominantly flow to the Northeast. A box core collected in the area beneath the wind axes (750m water depth) showed sub-millimeter to millimeter scale laminated sediments. Laminae were separated and analyzed for diatoms. Chronology was obtained by 210Pb dating. Three diatom associations were recognized in the sediments studied: a cold water association dominated by Thalasionema nitzschioides, T. nitzchioides var. parva, Lioloma pacificum and Chaetoceros spores; an association dominated by Fragilariopsis doliolus, T. bacillare and Thalassiosira oestrupii, more characteristic of temperate waters, and an association of warm waters characterized by Neodelphineis pelagica, T. pseudonitzschioides, Actinocyclus ellipticus, Cyclotella litoralis and Thalassiosira decipiens. Abundance of diatoms is higher (up to 344 106 valves g-1) in the coldest association and lowest (83 106 valves g-1) in the warmer one. Although upwelling species are present throughout the core, we observed a decrease in diatom abundance and an increase in temperate and warm water taxa from the 1960's-1970's. This trend is coincident with the climatic changes produced by the slowdown of the meridional overturning circulation proposed for the past century and global warming.

The influence of changes in nitrogen: silicon ratios on diatom growth dynamics

NASA Astrophysics Data System (ADS)

Gilpin, L. C.; Davidson, K.; Roberts, E.

2004-02-01

Nitrate loading to coastal waters has increased over recent decades while silicon loading has remained relatively constant or decreased. As the N:Si ratio in coastal waters shifts due to these anthropogenic influences, silicate limitation of diatom biomass may become a feature of the biogeochemistry in coastal waters especially in regions of reduced exchange. Two sets of nutrient enrichment mesocosm experiments were conducted in successive years using a natural planktonic assemblage obtained from the Trondheimsfjord, Norway. The inorganic nutrient concentrations at the start of the experiments were manipulated to give a variety of N:Si concentrations at ratios representative of current and possible future values, should N loading continue. In June 1999 experiments were conducted with a gradient of inorganic N:Si ratios (1:2, 1:1, 2:1, 4:1) to investigate the influence of low and high N:Si ratio conditions and to determine the conditions that would generate Si limitation of diatom growth. In June 2000, based on 1999 data, highly replicated experiments were conducted at N:Si ratios of 1:1 and 4:1 which were expected to result in N and Si limitation of diatom growth, respectively; statistical differences in cellular composition were recorded. N limitation of diatom biomass increase was observed under the three lowest N:Si ratios: particulate carbon (C) accumulation continued to occur following N exhaustion resulting in an increase in the organic C:N ratio. Silicate limitation of diatom biomass increase only occurred at the highest N:Si ratio of 4:1. Silicate exhaustion was followed by continued nitrate uptake for several days, at a slower rate than previously. The resulting increase in organic N was accompanied by an increase in organic C such that the C:N ratio of the organic material at the highest N:Si ratio failed to increase to the extent observed under the N limited conditions. Statistically significant differences in chlorophyll-a yield per unit nitrate, C:chlorophyll-a ratios, C:N ratio and diatom cell yield per unit nitrate or Si were observed in Si compared to N limited conditions. All mesocosms became dominated numerically and in terms of biomass by the diatom Skeletonema costatum. The potential implications of changing N and Si regimes in coastal waters are discussed.

Paleoceanography of the Gulf of Alaska during the past 15,000 years: results from diatoms, silicoflagellates, and geochemistry

USGS Publications Warehouse

Barron, John A.; Bukry, David; Dean, Walter E.; Addison, Jason A.; Finney, Bruce

2009-01-01

High-resolution records of diatoms, silicoflagellates, and geochemistry covering the past 15,000 years were studied in three cores from the Gulf of Alaska (GOA). Core EW0408-85JC in an oceanic setting on the Kayak Slope displays a paleoceanographic record similar to that at several locations on the California margin during deglaciation. Biologic productivity as reconstructed using geochemical and microfossil proxies increased abruptly during the Bølling–Alleröd (Bø–Al) warm interval (14.7–12.9 cal ka), declined during the Younger Dryas (YD) cold interval (12.9 to 11.7 cal kyr BP), and rose again during the earliest Holocene. At this site, the record after ~ 11 cal kyr BP is dominated by oceanic diatoms and silicoflagellates, with geochemical proxies displaying more subtle variation. Cores EW0408-66JC in the Yakobi Sea Valley near Cross Sound and EW0408-11JC in the Gulf of Esquibel contain an expanded, composite record along the southeast Alaskan margin. Core 66JC contains a detailed record of the Bø–Al and YD. Diatoms and silicoflagellates indicate that coastal upwelling and biosiliceous productivity were strong during the Bø–Al but declined during the YD. Sea ice-related diatoms increased in abundance during the YD, indicating cooler, but less productive waters. The glacial to biogenic marine sediment transition in core 11JC occurs at 1280 cmbsf (centimeters below sea floor), probably representing rising sea level and deglaciation early in the Bø–Al. Freshwater and sea-ice related diatoms are common in the lower part of the core (Bø–Al and YD), but upwelling-related diatoms and silicoflagellates quickly increased in relative abundance up-core, dominating the record of the past 11,000 years. Low oxygen conditions in the bottom water as reconstructed using geochemical proxies (U and Mo concentration) were most intense between ~ 6.5 and 2.8 cal kyr BP, the beginning of which is coincident with increases in abundance of upwelling-related diatoms. The records from these three cores jointly thus made it possible to reconstruct paleoclimatic and paleoceanographic conditions at high northern Pacific latitudes during the last 15 kyr.

Numerical evaluation of magnetic absolute measurements with arbitrarily distributed DI-fluxgate theodolite orientations

NASA Astrophysics Data System (ADS)

Brunke, Heinz-Peter; Matzka, Jürgen

2018-01-01

At geomagnetic observatories the absolute measurements are needed to determine the calibration parameters of the continuously recording vector magnetometer (variometer). Absolute measurements are indispensable for determining the vector of the geomagnetic field over long periods of time. A standard DI (declination, inclination) measuring scheme for absolute measurements establishes routines in magnetic observatories. The traditional measuring schema uses a fixed number of eight orientations (Jankowski et al., 1996).

We present a numerical method, allowing for the evaluation of an arbitrary number (minimum of five as there are five independent parameters) of telescope orientations. Our method provides D, I and Z base values and calculated error bars of them.

A general approach has significant advantages. Additional measurements may be seamlessly incorporated for higher accuracy. Individual erroneous readings are identified and can be discarded without invalidating the entire data set. A priori information can be incorporated. We expect the general method to also ease requirements for automated DI-flux measurements. The method can reveal certain properties of the DI theodolite which are not captured by the conventional method.

Based on the alternative evaluation method, a new faster and less error-prone measuring schema is presented. It avoids needing to calculate the magnetic meridian prior to the inclination measurements.

Measurements in the vicinity of the magnetic equator are possible with theodolites and without a zenith ocular.

The implementation of the method in MATLAB is available as source code at the GFZ Data Center Brunke (2017).

The effects of short-term and long-term learning on the responses of lateral intraparietal neurons to visually presented objects.

PubMed

Sigurdardottir, Heida M; Sheinberg, David L

2015-07-01

The lateral intraparietal area (LIP) is thought to play an important role in the guidance of where to look and pay attention. LIP can also respond selectively to differently shaped objects. We sought to understand to what extent short-term and long-term experience with visual orienting determines the responses of LIP to objects of different shapes. We taught monkeys to arbitrarily associate centrally presented objects of various shapes with orienting either toward or away from a preferred spatial location of a neuron. The training could last for less than a single day or for several months. We found that neural responses to objects are affected by such experience, but that the length of the learning period determines how this neural plasticity manifests. Short-term learning affects neural responses to objects, but these effects are only seen relatively late after visual onset; at this time, the responses to newly learned objects resemble those of familiar objects that share their meaning or arbitrary association. Long-term learning affects the earliest bottom-up responses to visual objects. These responses tend to be greater for objects that have been associated with looking toward, rather than away from, LIP neurons' preferred spatial locations. Responses to objects can nonetheless be distinct, although they have been similarly acted on in the past and will lead to the same orienting behavior in the future. Our results therefore indicate that a complete experience-driven override of LIP object responses may be difficult or impossible. We relate these results to behavioral work on visual attention.

Relationship of the Williams-Poulios and Manning-Rosen Potential Energy Models for Diatomic Molecules

NASA Astrophysics Data System (ADS)

Jia, Chun-Sheng; Liang, Guang-Chuan; Peng, Xiao-Long; Tang, Hong-Ming; Zhang, Lie-Hui

2014-06-01

By employing the dissociation energy and the equilibrium bond length for a diatomic molecule as explicit parameters, we generate an improved form of the Williams-Poulios potential energy model. It is found that the negative Williams-Poulios potential model is equivalent to the Manning-Rosen potential model for diatomic molecules. We observe that the Manning-Rosen potential is superior to the Morse potential in reproducing the interaction potential energy curves for the {{a}3 Σu+} state of the 6Li2 molecule and the {{X}1 sum+} state of the SiF+ molecule.

Isolation of a Diatom Frustule Fragment from the Lower Stratosphere (22-27Km)-EVIDENCE for a Cosmic Origin

NASA Astrophysics Data System (ADS)

Wainwright, Milton; Rose, Christopher E.; Baker, Alexander J.; Briston, J. K.; Wickramasinghe, N. Chandra

2013-03-01

Sampling of the stratosphere at heights between 22 and 27 km was carried out in the UK on 31st July 2013 using balloon-borne equipment carrying aseptically clean electron microscope stubs onto which aerosols were directly captured. The experiment revealed the presence of a diatom frustule captured from a height of >25km. On account of the very short residence time of particles of diatom size and mass at these heights, we argue for its incidence from space, with a probable origin in the watery environment of a comet.

Coulomb-stable triply charged diatomic: HeY3+

NASA Astrophysics Data System (ADS)

Wesendrup, Ralf; Pernpointner, Markus; Schwerdtfeger, Peter

1999-11-01

Accurate relativistic coupled-cluster calculations show that the triply charged species HeY3+ is a stable molecule and represents the lightest diatomic trication that does not undergo a Coulomb fragmentation into charged fragments. The diatomic potential-energy curve is approximated by an extended Morse potential, and vibrational-rotational constants for HeY3+ are predicted (Re=224.3 pm, D0=0.394 eV, ωe=437 cm-1, ωexe=15.8 cm-1, Be=0.877 cm-1). It is further shown that the He-Y3+ bond can basically be described as a charge-induced dipole interaction.

Dissolved organic matter reduces algal accumulation of methylmercury

USGS Publications Warehouse

Luengen, Allison C.; Fisher, Nicholas S.; Bergamaschi, Brian A.

2012-01-01

Dissolved organic matter (DOM) significantly decreased accumulation of methylmercury (MeHg) by the diatom Cyclotella meneghiniana in laboratory experiments. Live diatom cells accumulated two to four times more MeHg than dead cells, indicating that accumulation may be partially an energy-requiring process. Methylmercury enrichment in diatoms relative to ambient water was measured by a volume concentration factor (VCF). Without added DOM, the maximum VCF was 32 x 104, and the average VCF (from 10 to 72 h) over all experiments was 12.6 x 104. At very low (1.5 mg/L) added DOM, VCFs dropped by approximately half. At very high (20 mg/L) added DOM, VCFs dropped 10-fold. Presumably, MeHg was bound to a variety of reduced sulfur sites on the DOM, making it unavailable for uptake. Diatoms accumulated significantly more MeHg when exposed to transphilic DOM extracts than hydrophobic ones. However, algal lysate, a labile type of DOM created by resuspending a marine diatom in freshwater, behaved similarly to a refractory DOM isolate from San Francisco Bay. Addition of 67 μM L-cysteine resulted in the largest drop in VCFs, to 0.28 x 104. Although the DOM composition influenced the availability of MeHg to some extent, total DOM concentration was the most important factor in determining algal bioaccumulation of MeHg.

Diatom and silicoflagellate biostratigraphy for the late Eocene: ODP 1090 (sub-Antarctic Atlantic)

USGS Publications Warehouse

Barron, John A.; Bukry, David B.; Gersonde, Rainer

2014-01-01

Abundant and well-preserved diatoms and silicofl agellate assemblages are documented through a complete late Eocene sequence, ODP Hole 1090B, recovered from the southern Agulhas Ridge in the sub-Antarctic South Atlantic. A sequence of Cestodiscus (diatom) species occurrence events involving C. pulchellus var. novazealandica, C. fennerae, C. antarcticus, C. convexus, C. trochus, and C. robustus is tied with paleomagnetic stratigraphy and provides the basis of proposing a new diatom zonation for the latest middle Eocene to early Oligocene (~37.6–33.4 Ma) of the sub-Antarctic South Atlantic. Comparison with previously published diatom occurrence charts suggested this zonation should be applicable throughout the low latitude regions of the world’s oceans. Silicofl agellates belong to the Dictyocha hexacantha and the overlying Corbisema apiculata Zones. The late Eocene succession of silicofl agellate species is dominated by Naviculopsis (20–60%). Naviculopsis constricta and N. foliacea dominate the D. hexacantha Zone, followed by the N. constricta, then N. biapiculata in the C. apiculata Zone. Cold-water Distephanus is most abundant in the latest Eocene along with N. biapiculata. The tops of zonal guide fossils Dictyocha hexacantha and Hannaites quadria (both 36.6 Ma) and Dictyocha spinosa (37.1 Ma) are tied with paleomagnetic stratigraphy.

Diatom microfossils from cretaceous and eocene sediments contain native silica precipitating long-chain polyamines.

PubMed

Bridoux, M C; Ingalls, A E

2013-05-01

Organic molecules from known biological sources (biomarkers) that are preserved over geological time are critical tools in the study of past conditions and events on earth. Polar molecules are typically recycled rapidly in marine environments and do not survive burial within aquatic sediments in unambiguously recognizable form. As such, geological biomarkers are formed almost exclusively from precursor biomolecules that have been altered, limiting their utility as paleoproxies. Here, we report that nitrogen-rich aliphatic long-chain polyamines (LCPAs), biosynthesized by diatoms in species-specific assemblages for the precipitation of nanopatterned siliceous cell walls (frustules), are preserved unaltered in the oldest available diatom fossils dating to the Lower Cretaceous (early Albian, 115-110 Ma). We further show that the cumulative LCPA pool accounts for 60% of the total C and 80% of the total N preserved in the Cretaceous age sediments. We suggest that silica glass formation by diatoms constitutes an important preservation mechanism for source-specific, polar biomolecules, protecting them indefinitely by encapsulation within the silicified frustule. LCPAs are a unique, source-specific carbon and nitrogen archive of diatom biomass, offering a promising tool for reconstruction of global cycles of carbon and nitrogen over geological timescales. © 2013 Blackwell Publishing Ltd.

Evolution of Antifreeze Protein Genes in the Diatom Genus Fragilariopsis: Evidence for Horizontal Gene Transfer, Gene Duplication and Episodic Diversifying Selection

PubMed Central

Sorhannus, Ulf

2011-01-01

Hypotheses about horizontal transfer of antifreeze protein genes to ice-living diatoms were addressed using two different statistical methods available in the program Prunier. The role of diversifying selection in driving the differentiation of a set of antifreeze protein genes in the diatom genus Fragilariopsis was also investigated. Four horizontal gene transfer events were identified. Two of these took place between two major eukaryote lineages, that is from the diatom Chaetoceros neogracile to the copepod Stephos longipes and from a basidiomycete clade to a monophyletic group, consisting of the diatom species Fragilariopsis curta and Fragilariopsis cylindrus. The remaining two events included transfers from an ascomycete lineage to the proteobacterium Stigmatella aurantiaca and from the proteobacterium Polaribacter irgensii to a group composed of 4 proteobacterium species. After the Fragilariopsis lineage acquired the antifreeze protein gene from the basidiomycetes, it duplicated and went through episodic evolution, characterized by strong positive selection acting on short segments of the branches in the tree. This selection pattern suggests that the paralogs differentiated functionally over relatively short time periods. Taken together, the results obtained here indicate that the group of antifreeze protein genes considered here have a complex evolutionary history. PMID:22253534

Effects of Landscape Conditions and Management Practices ...

EPA Pesticide Factsheets

Lakes continue to face escalating pressures associated with land cover change and growing human populations. The U.S. EPA National Lakes Assessment, which sampled 1,028 lakes during the summer of 2007 using a probabilistic survey, was the first large scale effort to determine the condition of lakes across the country. In addition to broad trends, these data offer an abundance of new opportunities to examine biodiversity patterns, drivers of ecosystem change, and effectiveness of management practices that aim to reduce adverse effects of land cover change. Here, we use 2006 National Land Cover Data and sediment diatom samples collected from the tops of cores to examine how land cover at different spatial extents affects the habitat and diatom communities of lakes. We are examining the effects of land cover in basins, buffers in upstream networks, and buffers adjacent to 188 lakes in regions extending from the Mid-Atlantic to New England. Identifying relationships of diatom communities with land cover and physico-chemical parameters, along with generating stressor-response curves, will help with (1) developing diatom indicators responsive to anthropogenic impacts, (2) identifying how spatial locations of land cover affect lake conditions and diatoms, (3) informing future assessments and management efforts, and (4) characterizing potentially different patterns across regions and the effects of natural variation. Comparisons of study lakes to reference lake conditio

The role of life cycle processes on phytoplankton spring bloom composition: a modelling study applied to the Gulf of Finland

NASA Astrophysics Data System (ADS)

Lee, Soonmi; Hofmeister, Richard; Hense, Inga

2018-02-01

Diatoms are typical representatives of the spring bloom worldwide. In several parts of the Baltic Sea, however, cold-water dinoflagellates such as Biecheleria baltica have become dominant during the past decades. We have investigated the mechanisms behind this trend by using an ecosystem model which includes the life cycles of three main phytoplankton groups (diatoms, dinoflagellates and cyanobacteria). Coupled to a water column model we have applied the model system for the period 1981-2010 to the Gulf of Finland. In agreement with observations, the model results show an increasing trend in the proportion of dinoflagellates in the Gulf of Finland. Temperature and life cycle-related processes explain the relative increase of dinoflagellates and corresponding decrease of diatoms. Warming over the 30 years has enabled a head start of dinoflagellates by reducing the time lag between germination and growth of vegetative cells. Although diatoms have a much higher growth rate, they cannot compete with the high dinoflagellate concentrations that result from the inoculum. Diatoms will only dominate in years when the inoculum concentrations of dinoflagellates or the temperatures are low. Overall, the model results suggest that consideration of life cycle dynamics of competing phytoplankton groups may be crucial to understand trends and shifts in community composition.

Interactions of the Algicidal Bacterium Kordia algicida with Diatoms: Regulated Protease Excretion for Specific Algal Lysis

PubMed Central

Paul, Carsten; Pohnert, Georg

2011-01-01

Interactions of planktonic bacteria with primary producers such as diatoms have great impact on plankton population dynamics. Several studies described the detrimental effect of certain bacteria on diatoms but the biochemical nature and the regulation mechanism involved in the production of the active compounds remained often elusive. Here, we investigated the interactions of the algicidal bacterium Kordia algicida with the marine diatoms Skeletonema costatum, Thalassiosira weissflogii, Phaeodactylum tricornutum, and Chaetoceros didymus. Algicidal activity was only observed towards the first three of the tested diatom species while C. didymus proved to be not susceptible. The cell free filtrate and the >30 kDa fraction of stationary K. algicida cultures is fully active, suggesting a secreted algicidal principle. The active supernatant from bacterial cultures exhibited high protease activity and inhibition experiments proved that these enzymes are involved in the observed algicidal action of the bacteria. Protease mediated interactions are not controlled by the presence of the alga but dependent on the cell density of the K. algicida culture. We show that protease release is triggered by cell free bacterial filtrates suggesting a quorum sensing dependent excretion mechanism of the algicidal protein. The K. algicida / algae interactions in the plankton are thus host specific and under the control of previously unidentified factors. PMID:21695044

Interactions of the algicidal bacterium Kordia algicida with diatoms: regulated protease excretion for specific algal lysis.

PubMed

Paul, Carsten; Pohnert, Georg

2011-01-01

Interactions of planktonic bacteria with primary producers such as diatoms have great impact on plankton population dynamics. Several studies described the detrimental effect of certain bacteria on diatoms but the biochemical nature and the regulation mechanism involved in the production of the active compounds remained often elusive. Here, we investigated the interactions of the algicidal bacterium Kordia algicida with the marine diatoms Skeletonema costatum, Thalassiosira weissflogii, Phaeodactylum tricornutum, and Chaetoceros didymus. Algicidal activity was only observed towards the first three of the tested diatom species while C. didymus proved to be not susceptible. The cell free filtrate and the >30 kDa fraction of stationary K. algicida cultures is fully active, suggesting a secreted algicidal principle. The active supernatant from bacterial cultures exhibited high protease activity and inhibition experiments proved that these enzymes are involved in the observed algicidal action of the bacteria. Protease mediated interactions are not controlled by the presence of the alga but dependent on the cell density of the K. algicida culture. We show that protease release is triggered by cell free bacterial filtrates suggesting a quorum sensing dependent excretion mechanism of the algicidal protein. The K. algicida / algae interactions in the plankton are thus host specific and under the control of previously unidentified factors.

Are Diatoms "Green" Aluminosilicate Synthesis Microreactors for Future Catalyst Production?

PubMed

Köhler, Lydia; Machill, Susanne; Werner, Anja; Selzer, Carolin; Kaskel, Stefan; Brunner, Eike

2017-12-16

Diatom biosilica may offer an interesting perspective in the search for sustainable solutions meeting the high demand for heterogeneous catalysts. Diatomaceous earth (diatomite), i.e., fossilized diatoms, is already used as adsorbent and carrier material. While diatomite is abundant and inexpensive, freshly harvested and cleaned diatom cell walls have other advantages, with respect to purity and uniformity. The present paper demonstrates an approach to modify diatoms both in vivo and in vitro to produce a porous aluminosilicate that is serving as a potential source for sustainable catalyst production. The obtained material was characterized at various processing stages with respect to morphology, elemental composition, surface area, and acidity. The cell walls appeared normal without morphological changes, while their aluminum content was raised from the molar ratio n (Al): n (Si) 1:600 up to 1:50. A specific surface area of 55 m²/g was measured. The acidity of the material increased from 149 to 320 µmol NH₃/g by ion exchange, as determined by NH₃ TPD. Finally, the biosilica was examined by an acid catalyzed test reaction, the alkylation of benzene. While the cleaned cell walls did not catalyze the reaction at all, and the ion exchanged material was catalytically active. This demonstrates that modified biosilica does indeed has potential as a basis for future catalytically active materials.

Fungal parasites infect marine diatoms in the upwelling ecosystem of the Humboldt current system off central Chile.

PubMed

Gutiérrez, Marcelo H; Jara, Ana M; Pantoja, Silvio

2016-05-01

This is the first report of fungal parasitism of diatoms in a highly productive coastal upwelling ecosystem, based on a year-round time series of diatom and parasitic Chytridiomycota abundance in the Humboldt Current System off Chile (36°30.80'S-73°07.70'W). Our results show co-variation in the presence of Skeletonema, Thalassiosira and Chaetoceros diatoms with attached and detached chytrid sporangia. High abundance of attached sporangia was observed during the austral spring, coinciding with a predominance of Thalassiosira and Skeletonema under active upwelling conditions. Towards the end of austral spring, a decreasing proportion of attached sporangia was accompanied by a decline in abundance of Skeletonema and Thalassiosira and the predominance of Chaetoceros, suggesting specificity and host density dependence of chytrid infection. The new findings on fungal parasitism of diatoms provide further support for the inclusion of Fungi in the current model of the role played by the marine microbial community in the coastal ocean. We propose a conceptual model where Fungi contribute to controlling the dynamics of phytoplankton populations, as well as the release of organic matter and the transfer of organic carbon through the pelagic trophic web in coastal upwelling ecosystems. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Floating assembly of diatom Coscinodiscus sp. microshells.

PubMed

Wang, Yu; Pan, Junfeng; Cai, Jun; Zhang, Deyuan

2012-03-30

Diatoms have silica frustules with transparent and delicate micro/nano scale structures, two dimensional pore arrays, and large surface areas. Although, the diatom cells of Coscinodiscus sp. live underwater, we found that their valves can float on water and assemble together. Experiments show that the convex shape and the 40 nm sieve pores of the valves allow them to float on water, and that the buoyancy and the micro-range attractive forces cause the valves to assemble together at the highest point of water. As measured by AFM calibrated glass needles fixed in manipulator, the buoyancy force on a single floating valve may reach up to 10 μN in water. Turning the valves over, enlarging the sieve pores, reducing the surface tension of water, or vacuum pumping may cause the floating valves to sink. After the water has evaporated, the floating valves remained in their assembled state and formed a monolayer film. The bonded diatom monolayer may be valuable in studies on diatom based optical devices, biosensors, solar cells, and batteries, to better use the optical and adsorption properties of frustules. The floating assembly phenomenon can also be used as a self-assembly method for fabricating monolayer of circular plates. Copyright © 2012 Elsevier Inc. All rights reserved.

Morphology and Molecular Phylogeny of Peritrich Ciliate Epibionts on Pelagic Diatoms: Vorticella oceanica and Pseudovorticella coscinodisci sp. nov. (Ciliophora, Peritrichia).

PubMed

Gómez, Fernando; Wang, Lu; Lin, Senjie

2018-04-01

Consortia of the peritrich ciliate Vorticella oceanica and the planktonic diatom Chaetoceros coarctactus are reported from the South Atlantic Ocean. The morphologies of the constituent species were similar to their counterparts from other geographical regions, revealing a widespread distribution in tropical waters. Besides, we describe Pseudovorticella coscinodisci sp. nov. that lives on Coscinodiscus wailesii and other pelagic diatoms off Brazil. The zooids were 34-45μm long, and 19-30μm wide with a stalk too short to coil. The cell surface showed a reticulate pellicle with 18-19 and 11-12 rows above and below the aboral ciliary wreath, respectively. In the SSU rDNA phylogeny V. oceanica clustered between the clades of Vorticella and Pseudovorticella/Epicarchesium, and Pseudovorticella coscinodisci sp. nov. clustered as a sister group of Pseudovorticella paracratera and P. sinensis. The V. oceanica-C. coarctactus consortium likely represents an obligate species-specific mutualistic symbiosis as the constituents are not known as free-living forms. In contrast, the diatom hosts are known as free-living forms in the consortia of Pseudovorticella coscinodisci. The new molecular data and species description will be valuable dataset for future research on the diversity and ecological significance of ciliate-diatom epibiotic consortia. Copyright © 2018 Elsevier GmbH. All rights reserved.

Genome-scale model reveals metabolic basis of biomass partitioning in a model diatom

DOE PAGES

Levering, Jennifer; Broddrick, Jared; Dupont, Christopher L.; ...

2016-05-06

Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curatedmore » reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. Furthermore, the model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.« less

Attraction Pheromone of The Benthic Diatom Seminavis robusta: Studies on Structure-Activity Relationships.

PubMed

Lembke, Christine; Stettin, Daniel; Speck, Franziska; Ueberschaar, Nico; De Decker, Sam; Vyverman, Wim; Pohnert, Georg

2018-04-01

Recently the first pheromone of a marine diatom was identified to be the diketopiperazine (S,S)-diproline. This compound facilitates attraction between mating partners in the benthic diatom Seminavis robusta. Interestingly, sexualized S. robusta cells are attracted to both the natural pheromone (S,S)-diproline as well as to its enantiomer (R,R)-diproline. Usually stereospecificity is a prerequisite for successful substrate-receptor interactions, and especially pheromone perception is often highly enantioselective. Here we introduce a structure-activity relationship study, to learn more about the principles of pheromone reception in diatoms. We analyzed the activity of nine different diketopiperazines in attraction and interference assays. The pheromone diproline itself, as well as a pipecolic acid derived diketopiperazine with two expanded aliphatic ring systems, showed the highest attractivity. Hydroxylatoin of the aliphatic rings abolished any bioactivity. Diketopiperazines derived from acyclic amino acids were not attrative as well. All stereoisomers of both the diproline and the pipecolic acid derived diketopiperazine were purified by enantioselective high-performance liquid chromatography, and application in bioactivity tests confirmed that attraction pheromone perception in this diatom is indeed not stereospecific. However, the lack of activity of diketopiperazines derived from acyclic amino acids suggests a specificity that prevents misguidance to sources of other naturally occurring diketopiperazines.

Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi.

PubMed

Amato, Alberto; Sabatino, Valeria; Nylund, Göran M; Bergkvist, Johanna; Basu, Swaraj; Andersson, Mats X; Sanges, Remo; Godhe, Anna; Kiørboe, Thomas; Selander, Erik; Ferrante, Maria I

2018-06-01

Diatoms and copepods are main actors in marine food webs. The prey-predator interactions between them affect bloom dynamics, shape marine ecosystems and impact the energy transfer to higher trophic levels. Recently it has been demonstrated that the presence of grazers may affect the diatom prey beyond the direct effect of grazing. Here, we investigated the response of the chain-forming centric diatom Skeletonema marinoi to grazer cues, including changes in morphology, gene expression and metabolic profile. S. marinoi cells were incubated with Calanus finmarchicus or with Centropages typicus and in both cases responded by reducing the chain length, whereas changes in gene expression indicated an activation of stress response, changes in the lipid and nitrogen metabolism, in cell cycle regulation and in frustule formation. Transcripts linked to G protein-coupled receptors and to nitric oxide synthesis were differentially expressed suggesting involvement of these signalling transduction pathways in the response. Downregulation of a lipoxygenase in the transcriptomic data and of its products in the metabolomic data also indicate an involvement of oxylipins. Our data contribute to a better understanding of the gene function in diatoms, providing information on the nature of genes implicated in the interaction with grazers, a crucial process in marine ecosystems.