title: Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages.
abstract: Hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. The microbial communities and metabolic potential in these ecosystems are largely uncharacterized. Here, we present four single amplified genomes (SAGs) obtained from 8,219 m below the sea surface within the hadal ecosystem of the Puerto Rico Trench (PRT). These SAGs are derived from members of deep-sea clades, including the Thaumarchaeota and SAR11 clade, and two are related to previously isolated piezophilic (high-pressure-adapted) microorganisms. In order to identify genes that might play a role in adaptation to deep-sea environments, comparative analyses were performed with genomes from closely related shallow-water microbes. The archaeal SAG possesses genes associated with mixotrophy, including lipoylation and the glycine cleavage pathway. The SAR11 SAG encodes glycolytic enzymes previously reported to be missing from this abundant and cosmopolitan group. The other SAGs, which are related to piezophilic isolates, possess genes that may supplement energy demands through the oxidation of hydrogen or the reduction of nitrous oxide. We found evidence for potential trench-specific gene distributions, as several SAG genes were observed only in a PRT metagenome and not in shallower deep-sea metagenomes. These results illustrate new ecotype features that might perform important roles in the adaptation of microorganisms to life in hadal environments.
authors.affiliation: Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA.
authors.forename: Rosa
authors.initials: R
authors.lastname: León-Zayas
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Novotny
authors.affiliation: Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA.
authors.forename: Sheila
authors.initials: S
authors.lastname: Podell
authors.affiliation: National Geographic Society, Washington, DC, USA.
authors.forename: Charles M
authors.initials: CM
authors.lastname: Shepard
authors.affiliation: National Geographic Society, Washington, DC, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Berkenpas
authors.affiliation: Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia National Research Institute Higher School of Economics, St. Petersburg, Russia.
authors.forename: Sergey
authors.initials: S
authors.lastname: Nikolenko
authors.affiliation: Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.
authors.forename: Pavel
authors.initials: P
authors.lastname: Pevzner
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
authors.forename: Roger S
authors.initials: RS
authors.lastname: Lasken
authors.affiliation: Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA dbartlett@ucsd.edu.
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Bartlett
mesh_terms: D000064:Acclimatization; D001105:Archaea / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D001483:Base Sequence; D019641:DNA, Archaeal / Q000235:genetics; D017753:Ecosystem; D004734:Energy Metabolism / Q000502:physiology; D005227:Fatty Acids / Q000378:metabolism; D020745:Genome, Archaeal / Q000235:genetics*; D008055:Lipids / Q000096:biosynthesis; D054892:Metagenome / Q000235:genetics*; D008969:Molecular Sequence Data; D009792:Oceans and Seas; D011647:Puerto Rico; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013455:Sulfur / Q000378:metabolism; D014871:Water Microbiology
chemical_list: D019641:DNA, Archaeal; D005227:Fatty Acids; D008055:Lipids; D012336:RNA, Ribosomal, 16S; D013455:Sulfur