East Boothbay, Maine - Scientists at the Bigelow Laboratory Single Cell Genomics Center (SCGC) are part of a groundbreaking effort to use DNA sequencing of genomes isolated from single microbial cells to discover uncharted branches in the bacterial and archaeal tree of life. Part of an international collaboration led by the U.S. Department of Energy Joint Genome Institute (DOE JGI), their most recent findings in the exploration of the planet’s “microbial dark matter” were published online July 14, 2013 in the journal Nature.“Our analysis of disparate evolutionary offshoots, enabled by cutting-edge single cell genomics tools, shed new light on the history of life on Earth over the past 3.5 billion years,” said Dr. Ramunas Stepanauskas, SCGC Director and one of the paper’s authors.
“Conceptually, this is similar to the work of cosmologists, who study signals from distant galaxies to trace the 14 billion year history of the universe. One of our intriguing findings is that, even relatively recently, genes have been exchanged among all three main branches of the tree of life—Bacteria, Archaea, and Eukarya, underlying the significance of as yet poorly understood evolutionary mechanisms. “
“In cosmology, dark matter is said to account for the majority of mass in the universe; however, its presence is inferred by indirect effects, rather than detected through telescopes. The biological equivalent is ‘microbial dark matter,’ the pervasive, yet practically invisible, infrastructure of life on the planet, which can have profound influences on the most significant environmental processes from plant growth and health, to nutrient cycles in terrestrial and marine environments, the global carbon cycle, and possibly even climate processes,” said Dr. Eddy Rubin, DOE JGI Director.
“This is a powerful example of how we pioneer discovery, in that we can take a high throughput approach to
isolating and characterizing single genomes from complex environmental samples of millions of cells, to provide a profound leap of understanding the microbial evolution on our planet. This is really the next great frontier.”
“Microbes are the most abundant and diverse forms of life on Earth,” said Dr. Tanja Woyke, DOE JGI Microbial Program Head and senior author on the Nature publication. “They occupy every conceivable environmental niche from the extreme depths of the oceans to the driest of deserts. However, our knowledge about their habits and potential benefits has been hindered by the fact that the vast majority of these have not yet been cultivated in the laboratory. So we have only recently become aware of their roles in various ecosystems through cultivation-independent methods, such as metagenomics and single-cell genomics. What we are now discovering are unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the domains of life.”
The multi-institutional, collaborative microbial dark matter campaign targeted uncultivated cells from nine diverse habitats: Sakinaw Lake in British Columbia; the Etoliko Lagoon of western Greece; a sludge reactor in Mexico; the Gulf of Maine; off the north coast of Oahu, Hawaii, the Tropical Gyre in the south Atlantic; the East Pacific Rise; the Homestake Mine in South Dakota; and the Great Boiling Spring in Nevada. From these samples, the team laser-sorted 9,000 cells, from which they were able to reassemble and identify 201 distinct genomes, which then could be aligned to 28 major previously uncharted branches of the tree of life. The SCGC generated much of the amplified single cell DNA used in the study.
The team’s findings fell into three main areas in the effort to “seek out new life.” The first was the discovery of unexpected metabolic features. They observed certain traits in Archaea that previously only were seen in Bacteria, and vice-versa, including the code for a potent enzyme that bacteria commonly use, leading the authors to hypothesize that Archaea may deploy it as a defense mechanism against attacking Bacteria.
The second contribution arising from the work was the correct reassignment, or binning, of data of some 340 million DNA fragments from other habitats to the proper lineage. This course correction provides insights into how organisms function in the context of a particular ecosystem, as well as a much improved and more accurate understanding of the associations of newly discovered genes with resident life forms.
The third finding was the resolution of relationships within and between microbial phyla—the taxonomic ranking between domain and class—which led the team to propose two new superphyla, which are highly stable associations between phyla. The 201 genomes provided solid reference points, anchors for phylogeny—the lineage history of organisms as they change over time. The researchers are pursuing a more accurate characterization of these relationships so that they can better predict metabolic properties and other useful traits that can be expressed by different groups of microbes.
“For almost 20 years now we have been astonished by how little there is known about massive regions of the tree of life,” said Phil Hugenholtz, Director of the Australian Centre for Ecogenomics at The University of Queensland and another one of the paper’s authors. “This project is the first systematic effort to address this enormous knowledge gap. One of the most significant contributions is that, based on these data, we provided names for many of these lineages, which, like most star systems, were just numbered previously. For me, taxonomic assignment is important, as it welcomes in strangers and makes them part of the family. Yet this is just a start. We are talking about probably millions of microbial species that remain to be described.”
Cosmologists have only mapped half of one percent of the observable universe and the path ahead in environmental genomics is similarly daunting. “There is still a staggering amount of diversity to explore,” Woyke said. “To try to capture 50 percent of just the currently known phylogenetic diversity, we would have to sequence 20,000 more genomes, and these would have to be selected based on being members of underrepresented branches on the tree. And, to be sure, these are only what are known to exist.”
The Nature publication “Insights into the phylogeny and coding potential of microbial dark matter” builds upon a DOE JGI pilot project, the Genomic Encyclopedia of Bacteria and Archaea (GEBA: http://www.jgi.doe.gov/programs/GEBA/) and closely articulates with other international efforts such as the Microbial Earth Project, which aims to generate a comprehensive genome catalog of all archaeal and bacterial type strains (http://www.microbial-earth.org), and the Earth Microbiome Project (http://www.earthmicrobiome.org). More information about GEBA-MDM is available at: http://bit.ly/GEBA-MDM
Joining the DOE JGI and Bigelow Laboratory in authorship on the MDM paper are researchers from Bielefeld University, Germany; the University of California, Davis; the University of Technology, Sydney; University of British Columbia, the University of Nevada, Las Vegas; the University of Western Greece; Woods Hole Oceanographic Institution; University of Illinois at Urbana-Champaign; and the Australian Centre for Eco genomics of the University of Queensland, Australia.
Bigelow Laboratory for Ocean Sciences is an independent, non-profit center for global ocean research, ocean science education, and technology transfer. A recognized leader in Maine's emerging innovation economy, the Laboratory’s research ranges from microbial oceanography -- examining the biology in the world’s oceans at the molecular level -- to the large-scale biogeochemical processes that drive ocean ecosystems and global environmental conditions. More information is available at bigelow.org.
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter. DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.
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