How to use anvi'o in interactive mode specifically on WHOI's server
Coccolithophores, a group of calcifying marine phytoplankton within the phylum Haptophyta, play a significant role in marine biogeochemical cycles, particularly in those of carbon and sulfur. Emiliania huxleyi is one of the most abundant extant coccolithophore species in the ocean, typified by its cosmopolitan distribution and ability to form large blooms. Intra-specific variability in physiology (e.g. enzymatic rates, morphology, growth rates) of E. huxleyi has long been known in cultured isolates.
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).
Phytoplankton blooms are central to the ecology of Cape Cod Bay, where historically spring blooms of diatoms have been rapidly grazed, shuttling biomass through the food web. In more recent years, blooms of a haptophyte, Phaeocystis pouchetii have become more frequent in Cape Cod Bay. These organisms produce large gelatinous colonies, which prevents blooms of this haptophyte from being effectively grazed, hence reducing carbon cycling in the upper water column. We are partnering with the Center for Coastal Studies in Provincetown to find and study these blooms.
A central project aim is adaptation of a new single cell transcriptome (SCT) sequencing approach called SeqWell for analysis of natural microbial communities. The method addresses two overarching obstacles to microbial symbiosis investigations: 1) the requirement that symbionts be brought into culture for ‘omics analyses, and 2) time resolution limits on bulk approaches because populations are asynchronous. With enough SCTs, pseudotime methods can establish the time course of host and symbiont interactions.
Are you a recent (or not so recent) graduate with an interest in biological oceanography or marine biology? Do you have molecular biology experience in the lab? Are you curious to learn more about how molecular biology can be used to study environmental systems?
I am excited to announce that Carolyn Tepolt and I are looking to hire a joint research assistant (i.e. lab tech) to join our labs at the Woods Hole Oceanographic Institution.