Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments

PLoS One. 2014 May 5;9(5):e96449. doi: 10.1371/journal.pone.0096449. eCollection 2014.

Abstract

Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Ammonia / metabolism
  • Archaea / classification
  • Archaea / genetics*
  • Archaea / metabolism
  • Genome, Archaeal*
  • Geologic Sediments / microbiology*
  • Oxidation-Reduction
  • Phylogeny

Substances

  • Ammonia

Grant support

This study was supported by the Basic Science Research Program (2012R1A1A2A10039384) through the National Research Foundation of MEST (Ministry of Education, Science, and Technology), Marine and Extreme Genome Research Center Program of the MLTM (Ministry of Land, Transport, and Maritime Affairs), and the Energy Efficiency & Resources Core Technology Program (20132020000170) of the KETEP (Korea Institute of Energy Technology Evaluation and Planning) granted financial resource from the MTIE (Ministry of Trade, Industry & Energy), Republic of Korea. ELM was supported by NSF grant #DEB-0841999. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.