DOE/SC-0142 2012 Genomic Science Awardee Meeting X Bethesda, Maryland February 26-29, 2012 [Revised: March 1, 2012] Prepared for the Prepared by U.S. Department of Energy Biological and Environmental Research Information System Office of Science Oak Ridge National Laboratory Office of Biological and Environmental Research Oak Ridge, TN 37830 Germantown, MD 20874-1290 Managed by UT-Battelle, LLC For the U.S. Department of Energy http://genomicscience.energy.gov Under contract DE-AC05-00OR22725 Systems Biology Strategies and Technologies for Understanding Microbes, Plants, and Communities particle associated bacteria have smaller genomes that are enriched for transporters, depleted in regulatory components and encode a proteome with relatively less nitrogen content. Influence141 of Habitat on Diversity and Overall patterns of diversity and richness are significantly Evolution of Surface Ocean Microbes higher for bacterial communities collected on larger pore- size filters. Intra- and inter-relationships between sites based Andrew E. Allen1* ([email protected]), Lisa Z. Allen,1,2 on diversity measures suggest that larger size class or parti- Jonathan H. Badger,1 Christopher L. Dupont,1 John P. cle-associated bacterial communities and those that inhabit McCrow,1 Ian T. Paulsen,4 Mathangi Thiagarajan,5 Doug more productive waters are significantly more variable. 5 6 1 B. Rusch, Jed Fuhrman, Kenneth H. Nealson, Shibu This work was funded by the Office of Biological and Environmental Yooseph, and J. Craig Venter1 Research in the DOE Office of Science (DE-FC02-02ER63453) 1Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, Calif.; 2Scripps Institution of Oceanography, University of California-San Diego, La Jolla; 3Division of Biological Sciences, University of California-San Diego, La Jolla; 4Macquarie University, Influence142 of Nutrients and Currents on the Sydney, NSW, Australia; 5Informatics, J. Craig Venter 6 Genomic Composition of Microbes across an Institute, Rockville, Md.; and Marine and Environmental Upwelling Mosaic Biology, University of Southern California, Los Angeles 1,2 1 Project Goals: The development of computational tools Lisa Zeigler Allen, Andrew E. Allen * ([email protected]), 2,3 1 1 to assess and compare marine metagenomic samples on Eric E. Allen, Jonathan H. Badger, John P. McCrow, Ian the basis of phylogenetic and functional diversity, and to T. Paulsen,4 Liam D.H. Elbourne,4 Mathangi Thiagarajan,5 examine genome level adaptations to resource availability Doug B. Rusch,5 Kenneth H. Nealson,1 Shannon J. in different size classes of marine bacteria. The Global Williamson,1 and J. Craig Venter1 Ocean Survey (GOS) continues to sample and analyze marine microbial life around the world from the Sorcerer 1Microbial and Environmental Genomics, J. Craig II research vessel. Comparisons of microbial populations Venter Institute, San Diego, Calif.; 2Scripps Institution in the Indian Ocean to those found during GOS phase of Oceanography, University of California-San Diego, I have resulted in a better understanding of variation in La Jolla; 3Division of Biological Sciences, University of ecological niches available in marine surface waters. California-San Diego, La Jolla; 4Macquarie University, Sydney, NSW, Australia; and 5Informatics, J. Craig Venter In open ocean pelagic ecosystems bacterial cells account Institute, Rockville, Md. for approximately half of the organic biomass and bacterial activity is responsible for consumption of a large fraction of Project Goals: Our basic research program focused on photosynthetically-derived carbon. Genomic adaptations acquisition and analysis of marine microbial metagenomic that underlie bacterial physiological adaptations to environ- data and development of genomic analysis tools for broad, mental gradients such as latitude, temperature, productivity, external community use. Our Marine Metagenomic and particle association have not been clearly elucidated on Diversity effort generated and analyzed shotgun sequenc- a large scale. Through analyses of metagenomic data derived ing data from microbial communities sampled from >260 from size-fractionated bacterial communities, large scale sites around the world. Starting in the summer 2007 and phylogenomics, and genome size-normalized analyses of continuing until the winter of 2008, we initiated a series genomic contents we elucidate several fundamental adapta- of sampling efforts focused on the Southern California tions to environmental gradients in the surface ocean. Our Bight and California Current Ecosystem in collaboration results show that marine bacterioplankton in the surface with several groups. In the summer of 2007, this cruise ocean adapt to environmental variability in three ways; was done in collaboration with the California Coopera- molecular-level alterations, changes in overall genomic tive Oceanic Fisheries Investigations (CalCOFI) group content, and transitions in community structure. We report to evaluate metagenomics at select areas characterized on the influence of habitat on genomic properties such as by coastal upwelling. These samples are a contrast to the estimated genome size, gene family composition, transporter primarily open ocean sites of the GOS expedition due to repertoire, and carbon to nitrogen ratio of the predicted the upwelling of nutrient rich deep waters that enable an proteome. Small free-living picoplanktonic open-ocean increase in primary production at the surface. bacterioplankton compared to coastal, larger size-class, or * Presenting author 107 Systems Biology Strategies and Technologies Metagenomic datasets were generated from samples col- Project goals: Our basic research program focuses on lected along a coastal to open ocean transect between acquisition and analysis of marine microbial metagenomic Southern California Bight and California Current waters data and development of genomic analysis tools for broad, during a seasonal upwelling event, providing an opportunity external community use. Our Marine Metagenomic to examine the impact of episodic pulses of cold nutrient Diversity effort generated and analyzed shotgun sequenc- rich water into surface ocean microbial communities. The ing data from microbial communities sampled from >260 dataset consists of approximately 5.8 million predicted sites around the world. Here we used informatic and proteins across seven sites, from 3 different size classes: 0.1- single cell techniques to generate genomes for unculti- 0.8μm, 0.8-3.0μm, and 3.0-200.0μm. Taxonomic and meta- vated but abundant organisms, adding genomic context to bolic analyses suggest that sequences from the 0.1-0.8μm the metagenomes. size class correlated with their position along the upwelling mosaic. However, taxonomic profiles of bacteria from the Bacteria in the 16S rRNA clade SAR86 are among the most larger size classes (0.8-200μm) were less constrained by abundant uncultivated constituents of microbial assemblages habitat and characterized by an increase in Cyanobacteria, in the surface ocean for which little genomic information Bacteroidetes, Flavobacteria, and dsDNA viral sequences. is currently available. Bioinformatic techniques were used Functional annotation of transmembrane proteins indicate to assemble two nearly complete genomes from marine that sites comprised of organisms with small genomes have metagenomes and single-cell sequencing provided two an enrichment of transporters with substrate specificities for more partial genomes. Recruitment of metagenomic data amino acids, iron and cadmium; whereas, organisms with shows that these SAR86 genomes substantially increase our larger genomes have a higher percentage of transporters knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal for ammonium and potassium. Eukaryotic-type glutamine γ synthetase (GS) II proteins were identified and taxonomi- and divergent lineage of -proteobacteria, and the individual cally classified as viral, most closely related to the GSII in genomes display a temperature-dependent distribution. Mimivirus, suggesting that marine Mimivirus-like particles Modestly sized at 1.25–1.7 Mbp, the SAR86 genomes lack may have played a role in the transfer of GSII gene func- several pathways for amino-acid and vitamin synthesis as tions. Additionally, a Planctomycete bloom was sampled well as sulfate reduction, trends commonly observed in other from one upwelling site providing a rare opportunity to abundant marine microbes. SAR86 appears to be an aerobic assess the genomic composition of a marine Planctomycete chemoheterotroph with the potential for proteorhodopsin- population. The significant correlations observed between based ATP generation, though the apparent lack of a retinal genomic properties, community structure, and nutrient biosynthesis pathway may require it to scavenge exoge- availability provide insights into habitat-driven dynamics nously-derived pigments to utilize proteorhodopsin. The among oligotrophic versus upwelled marine waters adjoining genomes contain an expanded capacity for the degradation each other spatially. of lipids and carbohydrates acquired using a wealth of tonB- dependent outer membrane receptors. Like the abundant Publication planktonic marine bacterial clade SAR11, SAR86 exhibits 1. In Press: Lisa Zeigler Allen, Eric E. Allen, Jonathan H. metabolic streamlining, but also a distinct carbon compound Badger, John P. McCrow, Ian T. Paulsen, Liam D. H. specialization, possibly avoiding