Environmental Barcoding Reveals Massive Dinoflagellate Diversity in Marine Environments

Rowena F. Stern is with University of British Columbia, Ales Horak is with University of British Columbia, Rose L. Andrew is with University of British Columbia, Mary-Alice Coffroth is with State University of New York at Buffalo, Robert A. Andersen is with the Bigelow Laboratory for Ocean Sciences, Frithjof C. Küpper is with the Scottish Marine Institute, Ian Jameson is with CSIRO Marine and Atmospheric Research, Mona Hoppenrath is with the German Center for Marine Biodiversity Research, Benoît Véron is with University of Caen Lower Normandy and the National Institute for Environmental Studies, Fumai Kasai is with the National Institute for Environmental Studies, Jerry Brand is with UT Austin, Erick R. James is with University of British Columbia, Patrick J. Keeling is with University of British Columbia.Background -- Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known “species”, as a reference to measure the natural diversity in three marine environments. Methodology/Principal Findings -- In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. Conclusions/Significance -- COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.This project was funded by Genome Canada and the Canadian Barcode of Life Network. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o

Preventing Escherichia coli for deer hunters

Introduction: Escherichia coli is a pathogenic bacterium of major concern in the food processing industry. Scientists have made great strides in reducing the prevalence of E. coli in pork, beef, and chicken products, but there is hardly any research done on wild game meats such as venison. It may be possible to reduce the levels of E. coli in venison using spices like cinnamon and coffee. Purpose: This study is focused on reducing the amount of E. coli in venison by adding cinnamon and coffee grounds to the meat. Methods: Two treatments were applied to each meat sample in addition to positive and negative control samples. Three dilutions were prepared for each sample on culture plates for E coli, total colony, and yeast and mold. Three repetitions of each dilution were performed to ensure precise and accurate data was received. Results: 270 samples were tested for E. coli growth, of which, all averaged data sets revealed substantial growth, including those for the negative control set. It is worthy to note that the total amount of E. coli decreased over a period of 7 days yet there was no substantial difference from values initially received at the beginning of the experiment. Since the α-value for each plate type was above 0.05 which indicates a 95% confidence interval, we fail to reject the null hypothesis. Significance: Because we fail to reject the null hypothesis, this means that neither cinnamon or coffee is effective in reducing E. coli levels in venison