Marine Microbiology Initiative Environmental Metagenomics Sequencing Portfolio

Marine Microbiology Initiative Environmental Metagenomics Sequencing Portfolio

The overarching goals of the Environmental Metagenomics Sequencing Portfolio were to support discoveries of new microbial species and their viral counterparts; to enable the discoveries of new genes of ecological importance; and to better understand microbial biodiversity globally. Shotgun metagenomic sequencing revolutionized the field of marine microbial ecology beginning in the early 2000s, providing an unprecedented window into the vast taxonomic and functional diversity previously obscured during historical cultivation-dependent studies of the world’s oceans. Inspired by the early voyages of the H.M.S. Beagle and the Challenger Expedition in the 19^th century, the J. Craig Venter Institute (JCVI) embarked on a highly ambitious endeavor beginning in 2003 to characterize marine and terrestrial microbial community biodiversity using high-throughput DNA sequencing. The metagenomic sequencing of the Sargasso Sea (Venter et al., Science, 2004) was a landmark pilot study that demonstrated that shotgun metagenomics could be used to study marine microbial biodiversity. To understand marine microbial diversity at a global scale, JCVI, with funding from Marine Microbiology Initiative (Grant #448, awarded in 2004) and the U.S. Department of Energy, embarked on the Sorcerer II Global Ocean Sampling (GOS) Expedition and sequenced several billion bits of DNA from around the world.

The output of the Sorcerer II GOS Expedition included 6.3 billion base pairs of DNA sequence with over 6 million predicted proteins that vastly expanded the known protein universe at the time. Important bioinformatics methods were developed to analyze and manage the vast amounts of data, including methods to map where sequence fragments align relative to reference genomes to examine the biogeography and genomic variation of abundant marine microbes. The novel sequence data led to key discoveries of evolutionarily-related but geographically dispersed populations of marine bacteria, archaea and viruses, helping elucidate the distribution of microbes in the ocean. Additional important biological insights included the unique evolutionary diversity of unexpected light-driven energy-generation abilities (proteorhodopsins) and correlations among functional gene abundances and ocean nutrient and elemental levels.

Complementary shotgun metagenomic studies conducted at JCVI contributed to a wide range of marine microbial sequence data, the output of which included sequencing samples from additional GOS sites from understudied ocean regions including the Indian Ocean and French Polynesia (Grant #521.02, awarded in 2006) and unique sites within Botany Bay, Australia (Grant #1142, awarded in 2006) and Antarctic lakes (Grant #1554, awarded in 2007). Furthermore, sequencing techniques at the Broad Institute using bacterial artificial chromosomes (BACs) and fosmids were supported (Grant #1109, awarded in 2006) as a different means to uncover larger segments of DNA to link taxonomic information and functional gene content.

Collectively, shotgun metagenomic sequencing has been a disruptive technology that helped transform the field of marine microbial ecology and laid the groundwork for an exemplary metagenomic catalogue that continues to serve as rich reference datasets today. In the early 2000s, metagenomics was considered a risky undertaking because it was unclear whether useful data or novel insights could be gleaned from environmental microbes. Now, metagenomics serves as a foundational – almost routine – practice in the study of marine microbial communities.

Publications 

1. PLoS Biology: Ocean Metagenomics Collection - The results of the GOS expedition were published in as eight landmark papers in a special volume of PLoS Biology.
2. Burke, C., S. Kjelleberg, & T. Thomas. (2009). Selective extraction of bacterial DNA from the surfaces of macroalgae. Appl Environ Microbiol, 75(1), 252-256. doi: 10.1128/AEM.01630-08.
3. Yung, P. Y., C. Burke, M. Lewis, S. Egan, S. Kjelleberg, & T. Thomas. (2009). Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion. Nucleic Acids Res, 37(21), e144. doi: 10.1093/nar/gkp746.
4. Ng, C., M. Z. DeMaere, T. J. Williams, F. M. Lauro, M. Raftery, J. A. Gibson, C. Andrews-Pfannkoch, M. Lewis, J. M. Hoffman, T. Thomas, & R. Cavicchioli. (2010). Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica. ISME J, 4(8), 1002-1019. doi: 10.1038/ismej.2010.28.
5. Thomas, T., D. Rusch, M. Z. DeMaere, P. Y. Yung, M. Lewis, A. Halpern, K. B. Heidelberg, S. Egan, P. D. Steinberg, & S. Kjelleberg. (2010). Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J, 4(12), 1557-1567. doi: 10.1038/ismej.2010.74.
6. Burke, C., T. Thomas, M. Lewis, P. Steinberg, & S. Kjelleberg. (2011). Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis. ISME J, 5(4), 590-600. doi: 10.1038/ismej.2010.164.
7. Lauro, F. M., M. Z. DeMaere, S. Yau, M. V. Brown, C. Ng, D. Wilkins, M. J. Raftery, J. A. Gibson, C. Andrews-Pfannkoch, M. Lewis, J. M. Hoffman, T. Thomas, & R. Cavicchioli. (2011). An integrative study of a meromictic lake ecosystem in Antarctica. ISME J, 5(5), 879-895. doi: 10.1038/ismej.2010.185.