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Grants List

Grants

Courtesy of MBARI, Micromonas (false color)

Monterey Bay Aquarium Research Institute

Development of marine eukaryotic metagenomic methods

To support a collaborative team of researchers to address gaps in understanding about the diversity and ecology of the eukaryotic microorganisms in the sea, develop eukaryotic metagenomics methods, perform quality control experiments to assess sampling and sequencing biases, and synthesize ecological and sequence data. This intensive molecular and environmental investigation aimed to decipher key ecological interactions among the larger and particle-attached marine eukaryotes, bacteria and archaea through the development of novel, validated eukaryotic metagenomic tools of broad use to the research community.

Title: Development of marine eukaryotic metagenomic methods
Date Awarded: Nov 2007
Amount: $950,351
Term: 39 months
Grant ID: GBMF1668
Funding Area: Science, Marine Microbiology Initiative
 

Abstract

Discoveries of new and diverse groups of marine microbes and the potential capabilities encoded in the genomes of these organisms have tremendously influenced views on how marine microbial communities function. At the time this project was initiated in 2007, most of these discoveries came from whole genome sequencing of cultured bacteria and metagenomic sequencing of microbes less than 0.8 ­µm in diameter (primarily bacteria and archaea). Also in 2007, the depth of sequencing possible did not allow assembly of metagenomes into genome fragments. These studies revealed a wealth of protein and functional diversity yet left broad domains of marine microbial life virtually unexplored.

This project aimed for transformative discoveries using metagenomic and transcriptomic sequencing of microbes in larger size fractions, especially eukaryotic microbes. In addition to sequencing efforts, a comprehensive suite of environmental measurements were made along a Pacific Ocean gradient that traverses coastal waters and a highly productive region (which are key to California fisheries) and low nutrient North Pacific Gyre waters.

By developing novel methods for studying eukaryotic organisms and sampling both RNA and DNA from three size fractions, the study identified new groups of organisms and novel activities not previously known to some of the groups. The study also enabled understanding of the interactions between microbes from different domains of life (bacteria, archaea, and eukaryotes) as well as viruses and nutrients. Transcriptomic sequencing, which specifically selected for RNA from eukaryotes, proved the most straightforward to analyze with respect to proteins and taxa present. These data also supported the first targeted metagenomics studies of eukaryotes, wherein individual populations of marine phytoplankton were sorted, genomic information sequenced, and partial genome assemblies generated and analyzed. This revealed key information about the evolution of wild haptophyte, pelagophyte, and prasinophyte algae as well as biogeography of lineages within these groups. A large number of 18S rRNA and 16S rRNA gene sequences were also generated from environmental clone libraries built using DNA from the same sample set. Bioinformatic developments included pplacer, a now widely used tool for fast, rigorous analysis of gene sequences (PCR-derived, metagenomics or transcriptomic) on a reference tree. This tool was further implemented in a high-throughput pipeline for phylogenetic analysis of barcoded ribosomal RNA gene sequences known as PhyloAssigner in collaboration with the Giovannoni lab (Oregon State University).

Read more:

  1. Worden, A. Z., and A.E. Allen. 2010. The voyage of the microbial eukaryote. Current Opinion in Microbiology 13: 652-660.
    http://www.sciencedirect.com/science/article/pii/S1369527410001153
  2. Matsen, F.A., R. B. Kodner, and E. V. Armbrust. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11:538.
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098090/
  3. Cuvelier, M. L., A. E. Allen, A. Monier, J. P. McCrow, M. Messié, S. G. Tringe, T. Woyke, R. M. Welsh, T. Ishoey, J. H. Lee, B. J. Binder, C. L. DuPont, M. Latasa, C. Guigand, K. R. Buck, J. Hilton, M. Thiagarajan, E. Caler, B. Read, R. S. Lasken, F. P. Chavez, and A. Z. Worden. 2010. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences USA 107: 14,679-14,684.
    http://www.pnas.org/content/107/33/14679
  4. Demir-Hilton E., S. Sudek, M. L. Cuvelier, C. Gentemann, J. P. Zehr, and A. Z. Worden. 2011. Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. ISME J 5(7): 1095-1107.  http://www.ncbi.nlm.nih.gov/pubmed/21289652
  5. Kim, E., J. W. Harrison, S. Sudek, M. D. M. Jones, H. M. Wilcox, T. A. Richards, A. Z. Worden, and J.M. Archibald. 2011. Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proceedings of the National Academy of Sciences USA 108(4): 1496–1500. http://www.pnas.org/content/108/4/1496
  6. Monier A., R. M. Welsh, C. Gentemann, G. Weinstock, E. Sodergren, E. V. Armbrust, J. A. Eisen, and A. Z. Worden. 2011. Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology 14(1): 162-176.
    http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02576.x/abstract
  7. Worden, A. Z., J. Janouskovec, D. McRose, A. Engman, R. M. Welsh, S. Malfatti, S. G. Tringe, and P. J. Keeling. 2012. Global distribution of a wild alga revealed by targeted metagenomics. Current Biology 22(17): R675-R677.  http://www.cell.com/current-biology/abstract/S0960-9822%2812%2900879-2
  8. Raven, J. A. 2012. Algal biogeography: metagenomics shows distribution of a picoplanktonic pelagophyte. Current Biology 22(17): R682–R683. Comment on Worden et al. 2012. Current Biology 22(17): R675–R677. http://www.cell.com/current-biology/abstract/S0960-9822%2812%2900821-4
  9. Vergin, K. L., B. Beszteri, A. Monier, J. C. Thrash, A. H. Treusch, F. Kilpert, A. Z. Worden, and S. J. Giovannoni. 2013. High resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site as determined by phylogenetic placement of pyrosequences. ISME Journal 7: 1322–1332. http://www.nature.com/ismej/journal/v7/n7/full/ismej201332a.html
  10. Lin, Y. C., T. Campbell, C. C. Chung, G. Gong, K. P. Chiang, and A. Z. Worden. 2012. Distribution patterns and phylogeny of novel marine stramenopiles (MAST) in the North Pacific Ocean. Applied and Environmental Microbiology 78(9): 3387–3399. http://aem.asm.org/content/78/9/3387.short
  11. Orsi, W. D., J. M. Smith, H. M. Wilcox, J. E. Swalwell, P. Carini, A. Z. Worden, and A. E. Santoro. 2015. Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. ISME Journal. http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014260a.html
  12. Sudek, S., R. C. Everroad, A. Gehman, J. M. Smith, C. L. Poirier, F. P. Chavez, and A. Z. Worden. 2015. Cyanobacterial distributions along a physico-chemical gradient in the northeastern Pacific Ocean. Environmental Microbiology. http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12742/abstract

 

Other grants to Monterey Bay Aquarium Research Institute (4)

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