Draft Genome Sequence of Nitrosococcus oceani Strain NS58, a Marine Ammonia-Oxidizing Gammaproteobacterium Isolated from Tokyo Bay Sediment

Abstract

We report a draft genome sequence of Nitrosococcus oceani strain NS58, isolated from Tokyo Bay sediment. The genome sequence of strain NS58 was nearly identical (>99.99%) to those of other strains of N. oceani isolated from different ocean regions. Only nine single-nucleotide polymorphisms were identified between N. oceani ATCC 19707T and NS58.

High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution

“…Cells were checked under a light microscope at 1000× magnification routinely for uniform cell morphology [35]. As recently described by Dohra et al [32], N. oceani strain NS58 was isolated into pure culture from Tokyo Bay sediment at the West East end of the North Pacific Gyre, which is clockwise connected to the location of AFC27 by the Kuroshio and North Pacific currents as well as the California and North Equatorial Currents (Figure 1).…”

“…The Nitrosoccus oceani strains compared in this study were isolated from different gyres of the Atlantic and Pacific Oceans [32,53] (Figure 1). Strains of widely distributed marine bacterial species such as Prochlorococcus marinus or Photobacterium profundum but not Crocosphaera watsonii were found to exhibit moderate to high cross-species genomic diversity [54][55][56].…”

“…This and because we are generally interested in the evolution of molecular diversity in ammonia-oxidizing bacteria including N. oceani [1], we decided to determine the entire genome sequences and set out to examine the extent of genomic diversity within the N. oceani lineage by focusing on these four strains originally isolated from the Atlantic (C-107 and C-27) and the Pacific (AFC27 and AFC132) Oceans. While working on this project, Dohra et al [32] identified and published the draft sequence of N. oceani strain NS58 using as reference template the sequences of the four N. oceani genomes we had deposited in Genbank to make the data publicly available.…”

“…To strengthen the conclusions based on our genome analyses, we decided to realign the sequence reads of the NS58 genome publicly deposited by Dohra et al after publication [32] and included the alignment constructed with slightly different methods in our analysis. The strains' chromosomal genome sizes are similar to each other with sizes of about 3.5 Mb (Table 1).…”

“…This and the omnipresence of N. oceani in the world's oceans generated the question whether different strains of the species isolated from different oceanic gyres differed in their genomic contents; in particular, genes encoding the catabolic inventory that facilitates transformations of nitrogen compounds. In this work, the genomes of three strains from different oceanic locations isolated into pure culture (C-27, AFC27, and AFC132) were sequenced and comparatively analyzed together with the sequences of the recently published genome sequence of N. oceani strain NS58 [32] and the previously analyzed type strain C-107 (ATCC 19707 = JMC 30415 = BCRC 17464 = NCIMB 11848 [2,33]).…”