A5088804551- Diatoms and Algae Research
- Algal biology and biofuel production
- Marine and coastal ecosystems
- Microbial Community Ecology and Physiology
- Photosynthetic Processes and Mechanisms
- Wastewater Treatment and Nitrogen Removal
- Protist diversity and phylogeny
- Aquatic Ecosystems and Phytoplankton Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Advanced Proteomics Techniques and Applications
- Atmospheric and Environmental Gas Dynamics
- Marine Biology and Ecology Research
- Genomics and Phylogenetic Studies
- Environmental DNA in Biodiversity Studies
- Methane Hydrates and Related Phenomena
- Enzyme Catalysis and Immobilization
- Climate Change and Geoengineering
- Water Quality Monitoring and Analysis
- Atmospheric chemistry and aerosols
- Constructed Wetlands for Wastewater Treatment
- Ocean Acidification Effects and Responses
- Parasitic Infections and Diagnostics
- Membrane Separation Technologies
J. Craig Venter Institute
2015-2022
Moss Landing Marine Laboratories
2022
San Jose State University
2009-2022
Scripps Institution of Oceanography
2012-2017
University of California, San Diego
2013-2017
Imperial College London
2017
Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, ecology; this Community Page describes a resource 700 transcriptomes marine microbial help understand role in the world's oceans.
Significance As global CO 2 levels rise and fossil fuel abundance decreases, the development of alternative fuels becomes increasingly imperative. Biologically derived fuels, specifically those from microalgae, are promising sources, but improvements throughout production process required to reduce cost. Increasing lipid yields in microalgae without compromising growth has great potential improve economic feasibility. We report that disrupting catabolism is a practical approach increase...
In spite of attractive attributes, diatoms are underrepresented in research and literature related to the development microalgal biofuels. Diatoms highly diverse have substantial evolutionarily-based differences cellular organization metabolic processes relative chlorophytes. tremendous ecological success, with typically higher productivity than other algal classes, which may relate factors discussed this review. can accumulate lipid equivalently or a greater extent rapidly induce...
Abstract Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, implications nutrient utilization growth are poorly understood. Using a combination transcriptomics, proteomics, metabolomics, fluxomics, flux balance analysis to examine short-term shifts in model pennate diatom Phaeodactylum tricornutum , we obtained...
Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response to low Fe have either utilized continuous (24 hr) illumination or sampled single time day, missing any temporal dynamics. We profiled physiology, metabolite composition, global transcripts pennate diatom Phaeodactylum tricornutum during steady-state at low, intermediate, high levels dissolved over light:dark cycles, better...
A major challenge in the development of microalgal strains for large-scale production is optimization biomass accumulation and fuel-relevant molecules such as triacylglycerol. Selecting targets genetic manipulation approaches will require a fundamental understanding organization regulation carbon metabolic pathways these organisms. Functional genomic metabolomics data becoming easier to obtain process, however interpreting significance physiological context challenging since framework all...
Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization metabolic mechanisms within cell. The marine diatom Cyclotella cryptica, which was originally identified Aquatic Species Program, a promising strain large-scale bioproducts, such as omega-3 fatty acids. We sequenced nuclear genome methylome this oleaginous to identify genetic traits that enable substantial accumulation triacylglycerol. comprised highly...
The ecological prominence of diatoms in the ocean environment largely results from their superior competitive ability for dissolved nitrate (NO3 −). To investigate cellular and genetic basis diatom NO3 − assimilation, we generated a knockout reductase gene (NR-KO) model pennate Phaeodactylum tricornutum. In NR-KO cells, N-assimilation was abolished although transport remained intact. Unassimilated accumulated resulting swelling associated changes biochemical composition physiology. Elevated...
Summary Diatoms are one of the most productive and successful photosynthetic taxa on Earth possess attributes such as rapid growth rates production lipids, making them candidate sources renewable fuels. Despite their significance, few details mechanisms used to regulate carbon metabolism currently known, hindering metabolic engineering approaches enhance productivity. To characterize transcript level component regulation, genome‐wide changes in abundance were documented model diatom...
Summary Photoacclimation consists of short‐ and long‐term strategies used by photosynthetic organisms to adapt dynamic light environments. Observable photophysiology changes resulting from these have been in coarse‐grained models predict light‐dependent growth rates. However, the contribution broader metabolic network, relevant species‐specific fitness, is not accounted for simple models. We incorporated experimental data with genome‐scale modeling characterize organism‐level, model diatom...
Decarbonization of anthropogenic activities is progressing too slowly, creating an urgent need to actively remove carbon dioxide (CO2) from our atmosphere if we are prevent the most severe consequences a disrupted climate system. The marine environment offers several potential approaches for sequestering carbon, with iron-enhanced biological productivity being extensively studied. However, past iron addition studies were not primarily aimed at quantifying durability storage, nor did they...
Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua . The 50 Mbp haploid size of is nearly double that model Phaeodactylum tricornutum , but 30% smaller than closer relative Fragilariopsis cylindrus Diploid assembly, which was facilitated by low levels allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed long, syntenic contigs,...
Nearly half of carbon fixation and primary production originates from marine phytoplankton, much it occurs in episodic blooms upwelling regimes. Here, we simulated limited by nitrogen iron incubating Monterey Bay surface waters with subnutricline inorganic nutrients measured the whole-community transcriptomic response during mid- late-bloom conditions. Cell counts revealed that centric pennate diatoms (largely Pseudo-nitzschia Chaetoceros spp.) were major blooming taxa, but dinoflagellates,...
There are many potential approaches to marine carbon dioxide removal (mCDR), of which ocean iron fertilization (OIF) has the longest history study. However, OIF studies date were not primarily designed quantify durability (C) storage, nor how wise might be as an mCDR approach. To C sequestration, we introduce a metric called “centennial tonne,” defined 1,000 kg isolated from atmospheric contact for on average at least 100 years. We present activities needed assess scientific and...
With increasing water reuse applications and possible stringent regulations of phosphorus content in secondary tertiary effluent discharge Florida, USA, alternative technologies beyond conventional treatment processes require implementation to achieve low (P) nitrogen (N) concentrations. A pilot scale membrane bioreactor (MBR) system, operated adopted the University Cape Town (UCT) biological process for domestic wastewater. The system 280 days at a wastewater facility with total hydraulic...
Diatoms are major contributors to global primary production and their populations in the modern oceans affected by availability of iron, nitrogen, phosphate, silica, other trace metals, vitamins, infochemicals. However, little is known about role phosphorylation diatoms its regulation signaling. We report a total 2759 sites on 1502 proteins detected Phaeodactylum tricornutum. Conditionally phosphorylated peptides were at low iron (n = 108), during diel cycle 149), due nitrogen 137). Through...