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At least 37 records · Page 2

Remote Sensing of Diatom Bloom Succession

Marine diatoms are major biogeochemical and ecological “influencers” that contribute to a large fraction of the carbon export and supplying fisheries (Falkowski 2015). The fluxes of carbon transfer to the food web or to the deep ocean vary according to the stage of a diatom bloom (Du Toit 2018). Stages can be determined using inherent optical properties that reflect their physiological state, such as the chlorophyll fluorescence to particulate backscattering ratio (ChlF/b(sub bp), Cetinic et al. 2015). Identifying the bloom stage can potentially improve biogeochemical models of carbon export and fishery management. However, it is not yet possible to adequately determine the stage of phytoplankton blooms using satellites. Satellite-derived remote sensing reflectance R(sub rs)(𝜆) allow for remote identification of diatom blooms in the open ocean (Sathyendranath et al. 2004), and there are techniques to estimate the fluorescence quantum yield (𝜑) that, when high, can indicate the nutrient limitation that often takes place when blooms start to senesce (Behrenfeld et al. 2009). The goal of this study is to use the ratio between the normalized fluorescence line height from R(sub rs)(𝜆) (nFLH) and the particulate backscattering (b(sub bp)(443)) provided by satellites to identify exponentially growing and senescent diatom blooms from space.

Lange, Priscila K.↗

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua . The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum , but 30% smaller than closer relative Fragilariopsis cylindrus . Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.

09 BIOMASS FUELS↗

Spin-free formulation of the multireference driven similarity renormalization group: A benchmark study of first-row diatomic molecules and spin-crossover energetics

We report a spin-free formulation of the multireference (MR) driven similarity renormalization group (DSRG) based on the ensemble normal ordering of Mukherjee and Kutzelnigg (1997). This ensemble averages over all microstates of a given total spin quantum number, and therefore, it is invariant with respect to SU(2) transformations. As such, all equations may be reformulated in terms of spin-free quantities and they closely resemble those of spin-adapted closed-shell coupled cluster (CC) theory. The current implementation is used to assess the accuracy of various truncated MR-DSRG methods (perturbation theory up to third order and iterative methods with single and double excitations) in computing the constants of 33 first-row diatomic molecules. The accuracy trends for these first-row diatomics are consistent with our previous benchmark on a small subset of closed-shell diatomic molecules. We then present the first MR-DSRG application on transition-metal complexes by computing the spin splittings of the [Fe(H 2 O) 6 ] 2+ and [Fe(NH 3 ) 6 ] 2+ molecules. A focal point analysis (FPA) shows that third-order perturbative corrections are essential to achieve reasonably converged energetics. The FPA based on the linearized MR-DSRG theory with one- and two-body operators and up to a quintuple- ζ basis set predicts the spin splittings of [Fe(H 2 O) 6 ] 2+ and [Fe(NH 3 ) 6 ] 2+ to be –35.7 and –17.1 kcal mol –1 , respectively, showing good agreement with the results of local CC theory with singles, doubles, and perturbative triples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Green diatom mutants reveal an intricate biosynthetic pathway of fucoxanthin

Fucoxanthin is a major light-harvesting pigment in ecologically important algae such as diatoms, haptophytes, and brown algae (Phaeophyceae). Therefore, it is a major driver of global primary productivity. Species of these algal groups are brown colored because the high amounts of fucoxanthin bound to the proteins of their photosynthetic machineries enable efficient absorption of green light. While the structure of these fucoxanthin-chlorophyll proteins has recently been resolved, the biosynthetic pathway of fucoxanthin is still unknown. Here, we identified two enzymes central to this pathway by generating corresponding knockout mutants of the diatom Phaeodactylum tricornutum that are green due to the lack of fucoxanthin. Complementation of the mutants with the native genes or orthologs from haptophytes restored fucoxanthin biosynthesis. We propose a complete biosynthetic path to fucoxanthin in diatoms and haptophytes based on the carotenoid intermediates identified in the mutants and in vitro biochemical assays. It is substantially more complex than anticipated and reveals diadinoxanthin metabolism as the central regulatory hub connecting the photoprotective xanthophyll cycle and the formation of fucoxanthin. Moreover, our data show that the pathway evolved by repeated duplication and neofunctionalization of genes for the xanthophyll cycle enzymes violaxanthin de-epoxidase and zeaxanthin epoxidase. Brown algae lack diadinoxanthin and the genes described here and instead use an alternative pathway predicted to involve fewer enzymes. Our work represents a major step forward in elucidating the biosynthesis of fucoxanthin and understanding the evolution, biogenesis, and regulation of the photosynthetic machinery in algae.

59 BASIC BIOLOGICAL SCIENCES↗

Probing Nanoscale Chemical Environments of Zinc in Diatoms

Diatoms impact the biogeochemical cycling of zinc (Zn) due to elevated cellular Zn levels over other phytoplankton, and their strong biological uptake of Zn in the Southern Ocean sets the global distribution of Zn in ocean water columns. Past studies have revealed the abundance and spatial distribution of Zn in individual diatoms, while others have shown diverse Zn chemical species in whole-cell aggregates. However, intracellular and intercellular variations in Zn chemical forms remained unknown. For the first time, we applied a synchrotron X-ray nanoprobe to cultured diatoms (Phaeodactylum tricornutum and Chaetoceros muelleri) and resolved spatial heterogeneities of Zn chemistry. The result shows the partitioning of Zn between intracellular contents (soft parts) and frustules (mainly in the intracellular contents for P. tricornutum and similar Zn concentrations in the intracellular contents and frustules for C. muelleri). We found multiple Zn chemical species unevenly distributed within individual cells, where Zn–phosphoryl complexes were the most abundant followed by cysteine, histidine, biogenic silica, and carboxyl complexes. Cellular Zn species varied between individual organisms and were influenced by Zn availability. To our knowledge, this work presents the first X-ray measurements of trace metal speciation at sub-100 nm resolution in biological samples in their natural state. In conclusion, this research improves our ability to examine the biogeochemistry of Zn on the nanoscale and can help us understand the role of Zn in plankton growth and the Zn cycle in ocean waters.

36 MATERIALS SCIENCE↗

Synergistic Effect of Diatomic Mo-B Site Confined in Graphene-Like C 2 N Enables Electrocatalytic Nitrogen Reduction via Novel Mechanism

Structural modulation of active site with atomic-level precision is of great importance to meet the activity and selectivity challenges that electrocatalysts are commonly facing. In this work, we have designed a metal (M) - nonmetal (NM) diatomic site embedded in graphene-like C 2 N (denoted as Mo-B@C 2 N), where electrocatalytic N 2 reduction reaction (eNRR) was thoroughly explored using density functional theory combined with computational hydrogen electrode method. Compared to M-M diatomic sites, Mo-B site can generate pronounced synergistic effect that led to eNRR proceeding via a novel quasi-dissociative reaction mechanism that has not been reported relative to the conventional enzymatic, consecutive, distal, and alternating associative mechanism. This newly uncovered mechanism in which N-N bond scission takes place immediately after the first proton-coupled electron transfer (PCET) step (i.e., *NH-*N + H + + e – ® *NH 2 *N) has demonstrated much advantage in PCET process over the four conventional mechanism in terms of thermodynamic barrier, except that the adsorption of side-on *N 2 seemed thermodynamically unfavorable (DG ads = 0.61eV). Our results have revealed that the activation of inert NºN triple bond is dominated by π*-backdonation mechanism as a consequence of charge transfers from both B and Mo site, and unexpectedly, from the substrate C 2 N itself as well. Moreover, the hybrid Mo-B diatomic site demonstrated superior performance over either Mo-Mo or B-B site for driving eNRR. Furthermore, our study could provide insight into the delicate relationships among atomic site, substrate and electrocatalytic performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.

Kordia↗

Monte Carlo calculations of diatomic molecule gas flows including rotational mode excitation

The direct simulation Monte Carlo method was used to solve the Boltzmann equation for flows of an internally excited nonequilibrium gas, namely, of rotationally excited homonuclear diatomic nitrogen. The semi-classical transition probability model of Itikawa was investigated for its ability to simulate flow fields far from equilibrium. The behavior of diatomic nitrogen was examined for several different nonequilibrium initial states that are subjected to uniform mean flow without boundary interactions. A sample of 1000 model molecules was observed as the gas relaxed to a steady state starting from three specified initial states. The initial states considered are: (1) complete equilibrium, (2) nonequilibrium, equipartition (all rotational energy states are assigned the mean energy level obtained at equilibrium with a Boltzmann distribution at the translational temperature), and (3) nonequipartition (the mean rotational energy is different from the equilibrium mean value with respect to the translational energy states). In all cases investigated the present model satisfactorily simulated the principal features of the relaxation effects in nonequilibrium flow of diatomic molecules.

Yoshikawa, K. K.↗

The coupled states approximation for scattering of two diatoms

The paper presents a detailed development of the coupled-states approximation for the general case of two colliding diatomic molecules. The high-energy limit of the exact Lippman-Schwinger equation is applied, and the analysis follows the Shimoni and Kouri (1977) treatment of atom-diatom collisions where the coupled rotor angular momentum and projection replace the single diatom angular momentum and projection. Parallels to the expression for the differential scattering amplitude, the opacity function, and the nondiagonality of the T matrix are reported. Symmetrized expressions and symmetrized coupled equations are derived. The present correctly labeled coupled-states theory is tested by comparing its calculated results with other computed results for three cases: H2-H2 collisions, ortho-para H2-H2 scattering, and H2-HCl.

Heil, T. G.↗

Diatoms on earth, comets, Europa and in interstellar space

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 A, which is found to agree with the observed ultraviolet absorbance properties of interstellar grains. The observational data are reviewed, and the known properties of diatoms and bacteria are considered. 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.

Hoover, R. B.↗

The diatom Fragilariopsis cylindrus : A model alga to understand cold-adapted life

Diatoms are significant primary producers especially in cold, turbulent, and nutrient-rich surface oceans. Hence, they are abundant in polar oceans, but also underpin most of the polar food webs and related biogeochemical cycles. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a keystone species in polar oceans and sea ice because it can thrive under different environmental conditions if temperatures are low. In this perspective paper, we provide insights into the latest molecular work that has been done on F. cylindrus and discuss its role as a model alga to understand cold-adapted life.

59 BASIC BIOLOGICAL SCIENCES↗

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9

Marine diatoms are eukaryotic microalgae that play significant ecological and biogeochemical roles in oceans. They also have significant potential as organismal platforms for exploitation to address biotechnological and industrial goals. In order to address both modes of research, sophisticated molecular and genetic tools are required. We presented here new and improved methodologies for introducing CRISPRCas9 to the model diatom Phaeodactylum tricornutum cells and a streamlined protocol for genotyping mutant cell lines with previously unknown phenotypes. First, bacterialconjugation was optimized for the delivery of Cas9 by transcriptionally fusing Cas9 to a selectable marker by the 2A peptide. An episome cloning strategy using both negative and positive selection was developed to streamline CRISPR-episome assembly. Next, cell line picking and genotyping strategies, that utilize manual sequencing curation, TIDE sequencing analysis, and a T7 endonuclease assay, were developed to shorten the time required to generate mutants. Following this new experimental pipeline, both singlegene and two-gene knockout cell lines were generated at mutagenesis efficiencies of 48% and 25%, respectively. Lastly, a protocol for precise gene insertions via CRISPRCas9 targeting was developed using particle-bombardment transformation methods. Overall, the novel Cas9 episome design and improved genotyping methods presented here allow for quick and easy genotyping and isolation of Phaeodactylum mutant cell lines (less than 3 weeks) without relying on a known phenotype to screen for mutants.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of the Electrostatic Field due to the Surface Monolayer Metal Atoms on the Dissociation of Homonuclear Diatomic Gases in Gas-Metal Surface Reactions

The present paper examines the role of an electrostatic field generated by the outermost monolayer of metal ions prior to gas adsorption in aiding the dissociation of homonuclear diatomic gas molecules. The interaction of five homonuclear diatomic gases, Cl 2 , F 2 , H 2 , N 2 and O 2 , with several pure metals are examined using Coulomb’s law to calculate the attractive and repulsive forces between the electrons or ions in the gas molecule and the free surface metallic electrons or ions assuming a Bohr model. These calculations demonstrate that the total energy of the electrostatic fields from the metals can exceed the molecular binding energies of Cl 2 , F 2 , and O 2 at some distance from the metallic surface thereby suggesting that these gases interact primarily with the metallic surface in their atomic states after molecular bond dissociation prior to reaction. In contrast, H 2 and N 2 gases do not dissociate prior to reaching the metal surface due to the fact that the effective charge of the gas ions is less than the total electron charge at the outermost electronic shell. The present results correlate linearly with the electrochemical series standard reduction potential as well as with the Pauling electronegativity for several metals.

Gas-metal reactions↗

Cu Evolution over Bimetallic Cu‐Y/Beta Zeolite Under H 2 and Ethanol Atmospheres: Unveiling the Role of Diatomic Metal–Metal Interactions

Understanding the dynamic evolution of Cu species under varying environmental conditions is critical for addressing challenges related to the activity and the stability of copper‐based catalysts in thermo‐, photo‐, and electrocatalysis. However, metal–metal interactions between dual single atoms and their effects on Cu evolution after exposure to different environmental molecules remain underexplored. Herein, we synthesized bimetallic Cu‐Y/Beta catalysts with dual single‐atom Cu and Y sites and monometallic Cu‐Beta catalysts with isolated Cu sites in dealuminated Beta zeolites. By varying Cu and Y compositions, diatomic interactions were studied under H 2 and ethanol atmospheres. With 6 wt% Y loading, approximately 0.4 wt% of Cu species in Cu‐Y/Beta remained partially oxidized as Cu(I) after reduction in pure H 2 at 350 °C, in contrast to the full transition to metallic Cu observed in Cu‐Beta. Combining X‐ray absorption spectroscopy with kinetic studies revealed that metallic Cu became the predominant species after reduction with H 2 as Cu loading increased from 0.4 to 1.7 wt%, quadrupling the initial ethanol dehydrogenation rate and demonstrating the dominant role of Cu(0) sites. In conclusion, scanning transmission electron microscopy and density functional theory simulations indicated spatial proximity between dual single‐atom Cu and Y sites and elucidated Cu speciation controlled by diatomic interactions.

Copper↗

Spectroradiometric detection of competitor diatoms and the grazer Poteriochromonas in algal cultures

To address challenges in early detection of pond pests, we have extended a spectroradiometric monitoring method, initially demonstrated for measurement of pigment optical activity and biomass, to the detection of algal competitors and grazers. The method relies upon measurement and interpretation of pond reflectance spectra spanning from the visible into the near-infrared. Reflectance spectra are acquired every 5 min with a multi-channel, fiber-coupled spectroradiometer, providing monitoring of algal pond conditions with high temporal frequency. The spectra are interpreted via numerical inversion of a reflectance model, in which the above-water reflectance is expressed in terms of the absorption and backscatter coefficients of the cultured species, with additional terms accounting for the pigment fluorescence features and for the water-surface reflection of sunlight and skylight. With this method we demonstrate detection of diatoms and the predator Poteriochromonas in outdoor cultures of Nannochloropsis oceanica and Chlorella vulgaris, respectively. Further, the relative strength of these signatures is compared to microscopy and sequencing analysis. Spectroradiometric detection of diatoms is then further assessed on beaker-contained mixtures of Microchloropsis salina with Phaeodactylum tricornutum, Thalassiosira weissflogii, and Thalassiosira pseudonana, respectively, providing an initial evaluation of the sensitivity and specificity of detecting pond competitors.

09 BIOMASS FUELS↗

LBNL_DIATOMICS v1

LBNL_DIATOMICS is a software package developed by P. Zarzycki (Lawrence Berkeley National Laboratory) for computing isotopic effects in diatomic molecules using mass-dependent spectroscopic parameters obtained experimentally or from first principles. The package provides a streamlined pipeline from the potential energy surface to the equilibrium constant of an isotopic exchange reaction.

Zarzycki, Piotr [Lawrence Berkeley National Labora↗

Middle and Late-Holocene coastal environments of far Southeastern Russia as inferred from palynological and diatom data

Existing discontinuous palynological records from coastal and river valley exposures, with varying quality of radiocarbon control, suggested that the regional Holocene climate in southern areas of the Russian Far East was characterized by as many as 10 fluctuations in temperature and/or precipitation. In this study, palynological data from Zerkalnoye Lake, located on the western coast of the Sea of Japan, indicate a gradual decline in temperature through the Middle and Late-Holocene with a Holocene thermal maximum between 8800 and 5500 cal yr BP. Three wetter than present intervals, marked by an increase in Pinus koraiensis, occurred c. 3600–3500 cal yr BP, 2340–2050 cal yr BP, and 1830–1800 cal yr BP. The Zerkalnoye record shows the dominance of Quercus-broadleaf forests during the Middle and Early Holocene, although Quercus shows a gradual decrease as climate cooled during this interval. Diatom analysis of the Zerkalnoye sediments documents that the site was a shallow bay or coastal lagoon until c. 3540 cal yr BP. After that time, a freshwater lake was established, which had variable marine influences probably caused by sea level changes following deglaciation. The diatom data indicate a cool water interval between 2900 and 2580 cal yr BP, also noted in other sites in the region. Changes in the basin’s depositional environment do not affect the palynological record, indicating such sites can provide reliable paleovegetational and paleoclimatic records. In conclusion, the discrepancies of the various regional paleoclimatic scenarios indicate the need for the further collection of continuous records from coastal to alpine zones in this region of northeastern Asia.

Environmental sciences↗

Optimizing the Design of Diatom Biosilica-Targeted Fusion Proteins in Biosensor Construction for Bacillus anthracis Detection

In vivo functionalization of diatom biosilica frustules by genetic manipulation requires careful consideration of the overall structure and function of complex fusion proteins. Although we previously had transformed Thalassiosira pseudonana with constructs containing a single domain antibody (sdAb) raised against the Bacillus anthracis Sterne strain, which detected an epitope of the surface layer protein EA1 accessible in lysed spores, we initially were unsuccessful with constructs encoding a similar sdAb that detected an epitope of EA1 accessible in intact spores and vegetative cells. This discrepancy limited the usefulness of the system as an environmental biosensor for B. anthracis. We surmised that to create functional biosilica-localized biosensors with certain constructs, the biosilica targeting and protein trafficking functions of the biosilica-targeting peptide Sil3T8 had to be uncoupled. We found that retaining the ER trafficking sequence at the N-terminus and relocating the Sil3T8 targeting peptide to the C-terminus of the fusion protein resulted in successful detection of EA1 with both sdAbs. Homology modeling of antigen binding by the two sdAbs supported the hypothesis that the rescue of antigen binding in the previously dysfunctional sdAb was due to removal of steric hindrances between the antigen binding loops and the diatom biosilica for that particular sdAb.

59 BASIC BIOLOGICAL SCIENCES↗