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

Lin Wang,Martin G Klotz,Chee Kent Lim

doi:10.3390/microorganisms8050693

Abstract

The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world’s oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C–107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.

Highlights

Strains of the bacterium Nitrosococcus oceani are Gram-negative marine gammaproteobacteria in the family Chromatiaceae [1]
In contrast to Ward and O’Mullan [3] working with enrichment isolates sampled from diverse oceanic gyres, we succeeded in enriching several of these N. oceani isolates into pure cultures and the alignment and analysis of determined 16S rRNA gene sequences of strains C-107, C-27, AFC27, and AFC132 in pure culture yielded near identical sequences
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

Summary

Introduction

Strains of the bacterium Nitrosococcus oceani are Gram-negative marine gammaproteobacteria in the family Chromatiaceae [1]. Oceani strain C-107 is omnipresent in the world’s oceans [3] and the type strain of the species in a genus of exclusively obligate aerobic and ammonia-dependent chemolithoautotrophs belonging to the functional guild of “ammonia-oxidizing bacteria” (AOB). This ammonia-catabolic lifestyle provides the energy and reductant required for the assimilation of carbon from carbon dioxide as the sole carbon source [4,5,6]. The wide distribution of these complete nitrifiers has since been demonstrated for various habitats, so far, not identified in marine systems (e.g., [25,26,27,28])

Methods

Results

Conclusion