Going Deeper Metagenome of a Hadopelagic Microbial Community Emiley A Eloe1 Douglas W Fadrosh2 Mark Novotny2 Lisa Zeigler Allen2 Maria Kim3 Mary Jane Lombardo2 Joyclyn Yee Greenbaum2 Shibu Yooseph2 Eric E Allen1 4 Roger Lasken2 Shannon J Williamson3 Douglas H Bartlett1 1 Marine Biology Research Division Scripps Institution of Oceanography University of California San Diego La Jolla California United States of America 2 Microbial and Environmental Genomics J Craig Venter Institute La Jolla California United States of America 3 J Craig Venter Institute Rockville Maryland United States of America 4 Division of Biological Sciences University of California San Diego La Jolla California United States of America Abstract The paucity of sequence data from pelagic deep ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth In this study an analysis is presented of a large scale 454 pyrosequencing metagenomic dataset from a hadopelagic environment from 6 000 m depth within the Puerto Rico Trench PRT A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea In a number of instances all three deep metagenomes displayed similar trends but were most magnified in the PRT including enrichment in functions for two component signal transduction mechanisms and transcriptional regulation Overrepresented transporters in the PRT metagenome included outer membrane porins diverse cation transporters and di and tri carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate glyoxylate and dicarboxylate metabolism A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance as reflected in the large numbers of transporters present for their removal As a complement to the metagenome approach single cell genomic techniques were utilized to generate partial whole genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT Alphaproteobacteria Gammaproteobacteria Bacteroidetes and Planctomycetes The single cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes Through these multifaceted sequence approaches new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun drenched zones above Citation Eloe EA Fadrosh DW Novotny M Zeigler Allen L Kim M et al 2011 Going Deeper Metagenome of a Hadopelagic Microbial Community PLoS ONE 6 5 e20388 doi 10 1371 journal pone 0020388 Editor Francisco Rodriguez Valera Universidad Miguel Hernandez Spain Received February 2 2011 Accepted April 29 2011 Published May 24 2011 Copyright 2011 Eloe et al This is an open access article distributed under the terms of the Creative Commons Attribution License which permits unrestricted use distribution and reproduction in any medium provided the original author and source are credited Funding This work was supported by NSF grants EF 0801793 and EF 0827051 to D H B and a NAI APS Lewis and Clark Fund for Exploration and Field Research in Astrobiology to E A E The funders had no role in study design data collection and analysis decision to publish or preparation of the manuscript Competing Interests The authors have declared that no competing interests exist E mail dbartlett ucsd edu refractory dissolved organic material The microbial biomass is largely supported by organic carbon availability which is mainly distributed as either aggregated or dissolved sinking material exported to depth via the biological pump from the productive surface waters 8 The microbial loop which is well documented to exert a major influence on a variety of biogeochemical cycles in surface waters is largely unknown in the dark ocean 9 10 Current information on the genomic attributes of deep sea microorganisms from non reducing environments has come mostly from two sources The first is the genome sequences obtained from piezophilic high pressure adapted bacterial species 11 12 13 Whole genome sequence data has indicated thus far an improved capacity for complex organic polymer utilization large numbers of transposable elements a high ratio of rRNA operon copies per genome and larger than average intergenic regions 12 The cultivated deep ocean bathytypes have an opportunistic r strategy lifestyle allowing rapid response Introduction Although at one time deep oceanic environments were considered to be devoid of life it is now well appreciated that such settings are part of the largest fraction of the biosphere harboring the greatest numbers and diversity of aquatic microorganisms 1 Yet despite their significance deep ocean environments remain poorly sampled One reflection of this is that the Global Ocean Sampling GOS Expedition alone has surveyed the metagenomes of 52 surface water locations 2 3 4 but only two pelagic deep seawater metagenome studies have been performed to date 5 6 7 Pelagic deep ocean environments are distinguished from their shallow water counterparts in a number of fundamental physical characteristics including the absence of sunlight low temperature and increased pressure with depth Additionally the chemical constituents of the deep ocean consist of high inorganic nutrient concentrations such as nitrate and phosphate and PLoS ONE www plosone org 1 May 2011 Volume 6 Issue 5 e20388 Deep Trench Metagenome and Single Cell Genomics to environmental changes and a greater level of gene regulation 12 While these confirmed piezophilic isolates are restricted to only a narrow phylogenetic grouping the lifestyle strategies observed could reflect similar adaptive mechanisms across a wide range of phylogenetic types It has recently been suggested that deep ocean microbial communities harbor functional properties indicative of copiotrophs separate from the streamlined high recruiting genomes found to dominate in oligotrophic surface seawater 3 The second source of information on the genomic characteristics of deep sea microorganisms consists of metagenomic