title: Metatranscriptome profiling of a harmful algal bloom.
abstract: Metagenomic methods provide a powerful means to investigate complex ecological phenomena. Developed originally for study of Bacteria and Archaea, the application of these methods to eukaryotic microorganisms is yet to be fully realized. Most prior environmental molecular studies of eukaryotes have relied heavily on PCR amplification with eukaryote-specific primers. Here we apply high throughput short-read sequencing of poly-A selected RNA to capture the metatranscriptome of an estuarine dinoflagellate bloom. To validate the metatranscriptome assembly process we simulated metatranscriptomic datasets using short-read sequencing data from clonal cultures of four algae of varying phylogenetic distance. We find that the proportion of chimeric transcripts reconstructed from community transcriptome sequencing is low, suggesting that metatranscriptomic sequencing can be used to accurately reconstruct the transcripts expressed by bloom-forming communities of eukaryotes. To further validate the bloom metatransciptome assembly we compared it to a transcriptomic assembly from a cultured, clonal isolate of the dominant bloom-causing alga and found that the two assemblies are highly similar. Eukaryote-wide phylogenetic analyses reveal the taxonomic composition of the bloom community, which is comprised of several dinoflagellates, ciliates, animals, and fungi. The assembled metatranscriptome reveals the functional genomic composition of a metabolically active community. Highlighting the potential power of these methods, we found that relative transcript abundance patterns suggest that the dominant dinoflagellate might be expressing toxin biosynthesis related genes at a higher level in the presence of competitors, predators and prey compared to it growing in monoculture.
authors.affiliation: CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA.
authors.forename: Endymion D
authors.initials: ED
authors.lastname: Cooper
authors.affiliation: CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA.
authors.forename: Bastian
authors.initials: B
authors.lastname: Bentlage
authors.affiliation: CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA.
authors.forename: Theodore R
authors.initials: TR
authors.lastname: Gibbons
authors.affiliation: Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E Pratt St., Baltimore, MD 21202, USA.
authors.forename: Tsvetan R
authors.initials: TR
authors.lastname: Bachvaroff
authors.affiliation: CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA ; Maryland Agricultural Experiment Station, AGNR, University of Maryland, College Park, MD 20742, USA.
authors.forename: Charles F
authors.initials: CF
authors.lastname: Delwiche
keywords: De novo assembly; Dinoflagellate; Flow cytometry; Harmful algal bloom; Metagenomics; Metatranscriptomics; Prorocentrum minimum; Transcriptomics