Metatranscriptomics is a useful probe into the members of an ecological community, capturing community members and their potential functions in a single sequencing effort. Because transcribed RNA is sequenced, via thorough processing of metatrancriptomes, we can decipher both the members constituting a community as well as the genes that each member was expressing at the instant that the sample was collected. Metatranscriptomics is a relatively immature pursuit as compared to genomics or transcriptomics.
Easy, accurate classification of the taxonomy of microbial eukaryotes in the environment is a persistent challenge. For metagenomic and metatranscriptomic data, annotation is imperfect, because genomic references for organisms isolated from the environment are lacking. By leveraging experimental transcriptomic references, we have designed a tool to estimate the taxonomy of marine microbial eukaryotes. The tool is a flexible and modular way to leverage the expanding amount of omics data on environmentally-isolated microbial eukaryotes in order to better annotate multi-organism omics datasets (meta-omics).
Emiliania huxleyi is a globally-distributed coccolithophore with a major influence on beogeochemical cycling via the production of large, ephemeral blooms. Because of its global distribution, Emiliania huxleyi has a wide thermal range and apparently a high capacity for short-term acclimation and long-term adaptation to thermal conditions. We are studying this capacity in the lab via both traditional experimental acclimation approaches in semi-continuous culture, and via tracking gene expression changes in response to thermal conditioning in the taxon via transcriptomics.
The marine eukaryotic alga *Heterosigma akashiwo* (Raphidophyceae) is known for forming ichthyotoxic harmful algal blooms (HABs). In the past 50 years, *H. akashiwo* blooms have increased, occurring globally in highly eutrophic coastal and estuarine …
The concentration and composition of bioavailable nitrogen (N) and phosphorus (P) in the upper ocean shape eukaryotic phytoplankton communities and influence their physiological responses. Phytoplankton are known to exhibit similar physiological …
Marine eukaryotic phytoplankton adapt to low phosphorus (P) in the oceans through a variety of step‐wise mechanisms including lipid substitution and decreased nucleic acid content. Here, we examined the impact of low P concentrations on intracellular …
Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of …
Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. …
Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on …