Ariel Rabines
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View article: Relationships between phytoplankton pigments and DNA- or RNA-based abundances support ecological applications
Relationships between phytoplankton pigments and DNA- or RNA-based abundances support ecological applications Open
Observations of phytoplankton abundances and community structure are critical towards understanding marine ecosystems. Common approaches to determine group-specific abundances include measuring phytoplankton pigments with high-performance …
View article: Complete genome sequence of bacteriophages Merry and Sunny infecting <i>Microbacterium chocolatum</i> strain <i>GAI20246-6</i> isolated from an outdoor commercial algal pond
Complete genome sequence of bacteriophages Merry and Sunny infecting <i>Microbacterium chocolatum</i> strain <i>GAI20246-6</i> isolated from an outdoor commercial algal pond Open
We report the isolation of two virulent phages from an outdoor algal pond infecting the bacteria Microbacterium chocolatum strain GAI20246-6. Their genomes are both 53.6kb with a GC content of 67.8%. Some genomic features are described as …
View article: Marine microbial mock communities for validating rRNA gene amplicon sequencing
Marine microbial mock communities for validating rRNA gene amplicon sequencing Open
Mock communities are defined mixtures of cells or DNA for methods development, testing, or validation. Here, we present mock communities based on previously used 16S and 18S rRNA gene sequences from diverse marine microorganisms. Their use…
View article: Relationships between phytoplankton pigments and DNA- or RNA-based abundances support ecological applications
Relationships between phytoplankton pigments and DNA- or RNA-based abundances support ecological applications Open
Observations of phytoplankton abundances and community structure are critical towards understanding marine ecosystems. Common approaches to determine group-specific abundances include measuring phytoplankton pigments via high-performance l…
View article: Molecular forecasting of domoic acid during a pervasive toxic diatom bloom
Molecular forecasting of domoic acid during a pervasive toxic diatom bloom Open
In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia…
View article: Phytoplankton growth and grazing dynamics during anomalous heat wave and suppressed upwelling conditions in the southern California Current
Phytoplankton growth and grazing dynamics during anomalous heat wave and suppressed upwelling conditions in the southern California Current Open
We investigated phytoplankton dynamics in the southern California Current System (SCCS) in August 2014 during the early phase of the 2014-15 marine heat wave (MHW). Multi-day experiments were conducted at three inshore and two offshore sit…
View article: 16S and 18S rRNA mock community construction v1
16S and 18S rRNA mock community construction v1 Open
Mock communities are defined mixtures of cells or DNA for methods development, testing, or validation. Here we present mock communities based on previously used 16S and 18S rRNA gene sequences from diverse marine microorganisms. Their use …
View article: Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom
Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom Open
In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia…
View article: High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones
High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones Open
Ocean microbes are the foundation of marine food webs, regulating carbon cycling and ecosystem dynamics. How they proliferate, die, move, and interact is regulated by physical, chemical, and biological factors that are dynamic and challeng…
View article: Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton
Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton Open
Supplementary Figure 17: Maximum likelihood phylogenetic tree as inferred from iron permease (FTR1) amino acid sequences (255 taxa/241 positions) under the LG+C40+F+R8 model as implemented in IQTree 2. The scale bar represents 0.1 amino ac…
View article: Illuminating the dark metabolome of <i>Pseudo‐nitzschia</i> –microbiome associations
Illuminating the dark metabolome of <i>Pseudo‐nitzschia</i> –microbiome associations Open
The exchange of metabolites mediates algal and bacterial interactions that maintain ecosystem function. Yet, while thousands of metabolites are produced, only a few molecules have been identified in these associations. Using the ubiquitous…
View article: Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom Open
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 ne…
View article: Pathogenic <i>Vibrio</i> Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Pathogenic <i>Vibrio</i> Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes Open
Many species of coastal vibrio bacteria can infect humans, representing a growing health threat linked to increasing seawater temperatures. However, their interactions with surrounding microbes in the environment, especially eukaryotic org…
View article: Diploid Genomic Architecture of Nitzschia Hildebrandi, An Elite Biomass Production Diatom
Diploid Genomic Architecture of Nitzschia Hildebrandi, An Elite Biomass Production Diatom Open
A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia hildebrandi . The 50 Mbp haploid size of the nuclear genome is ne…
View article: Coastal Microbiomes Reveal Associations between Pathogenic&nbsp;Vibrio&nbsp;Species, Environmental Factors, and Planktonic Communities
Coastal Microbiomes Reveal Associations between Pathogenic Vibrio Species, Environmental Factors, and Planktonic Communities Open
Background Many species of coastal Vibrio spp. bacteria can infect humans, representing an emerging health threat linked to increasing seawater temperatures. Vibrio interactions with the planktonic community impact coastal ecology and huma…
View article: Amplicon Library Preparation v1
Amplicon Library Preparation v1 Open
18S and 16S amplicon library preparation protocol. DNA or RNA is usually extracted with our automated protocols from sterivex but other types of samples are occasionally used. If using RNA, first generate cDNA with Invitrogen's SuperScript…
View article: NOAA-CalCOFI Ocean Genomics (NCOG) Sample Collection v1
NOAA-CalCOFI Ocean Genomics (NCOG) Sample Collection v1 Open
This protocol describes our sampling strategy and techniques for the NOAA-CalCOFI Ocean Genomics (NCOG) project. In summary, seawater for DNA and RNA from multiple depths is filtered onto Sterivex filters at each station. Although the prot…
View article: Microbiomes of pathogenic Vibrio species reveal environmental and planktonic associations
Microbiomes of pathogenic Vibrio species reveal environmental and planktonic associations Open
Background Many species of coastal Vibrio spp. bacteria can infect humans, representing an emerging health threat linked to increasing seawater temperatures. Vibrio interactions with the planktonic community impact coastal ecology and huma…
View article: Measurements of nitrogen fixation in the oligotrophic North Pacific Subtropical Gyre using a free-drifting submersible incubation device
Measurements of nitrogen fixation in the oligotrophic North Pacific Subtropical Gyre using a free-drifting submersible incubation device Open
One challenge in field-based marine microbial ecology is to achieve sufficient spatial resolution to obtain representative information about microbial distributions and biogeochemical processes. The challenges are exacerbated when conducti…