Abstract
Strain IMCC3088, cultivated from the Yellow Sea, is a novel isolate belonging to the OM60/NOR5 clade and is closely related to clone OM241, Congregibacter litoralis, and strain HTCC2080. Here, the genome sequence of strain IMCC3088 is presented, showing the absence of photosynthetic gene clusters and the presence of proteorhodopsin.
GENOME ANNOUNCEMENT
The OM60/NOR5 clade, part of the oligotrophic marine Gammaproteobacteria group, comprises up to 11% of the bacterial communities on the ocean surface (3, 5, 6, 9). This important marine clade includes Congregibacter litoralis (6, 7) and extinction cultures designated HTCC2080, HTCC2148, and HTCC2246 (3, 4), in addition to several uncharacterized marine oligotrophic bacteria. Full genomic analyses of two representative strains (HTCC2080 and C. litoralis KT71) in the OM60/NOR5 clade have shown that they are aerobic anoxygenic phototrophs (AAnP) harboring photosynthetic gene clusters (puf) (4, 6). However, genome analyses of strain HTCC2148 (8), a member of the NOR5-8 subclade (9), showed the absence of photosynthetic gene clusters in the genome, indicating that there would be more diverse metabolism other than AAnP in the OM60/NOR5 clade.
Strain IMCC3088 was isolated from a surface seawater sample collected from the Yellow Sea off the coast of Incheon, South Korea, by using standard dilution techniques on an oligotrophic medium, marine 1/10R2A. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC3088 belongs to the NOR5-4 subclade (9) of the OM60/NOR5 clade, which contains OM241 (U70702) and DS029 (DQ234113). The strain is also closely related to cultured marine isolates of C. litoralis KT71 (94.8%), Haliea rubra CM41-15a (94.7%), and strain HTCC2080 (93.9%). Strain IMCC3088 was chosen for genome sequencing to reveal diverse metabolic potential in the OM60/NOR5 clade.
Whole-genome shotgun sequencing of strain IMCC3088 was performed by Macrogen, Inc. (Seoul, South Korea), with library construction using 5 μg genomic DNA based on Solexa paired-end sequencing technology (2). A total of 7,015,036 short reads were generated, reaching a depth of 86-fold genome coverage, and assembled into 183 contigs (AEIG01000001 to AEIG01000183) by using Velvet (10). The unclosed draft genome of IMCC3088 has 3,045,708 bases with a mean G+C content of 51.64%. Annotation of the open reading frames (ORFs) and noncoding RNAs was performed by using the RAST (rapid annotation using subsystem technology) server (1), and predicted ORFs were cross-checked with the COG, KEGG, and SwissProt databases. The IMCC3088 genome has 2,858 predicted ORFs, one copy each of the 5S, 16S, and 23S rRNA genes, and 34 predicted tRNAs.
In contrast to the existence of a puf operon in C. litoralis KT71 and HTCC2080, there are no predicted puf genes in the genome of IMCC3088. Instead, the IMCC3088 genome is predicted to encode proteorhodopsin, followed by the gene clusters for the biosynthesis of the retinal chromophore of rhodopsin (crtEIBY), suggesting that proteorhodopsin is functional. Strain IMCC3088 could be the first bacterium that harbors proteorhodopsin among the members of the OM60/NOR5 clade, indicating the existence of diverse metabolic potential in the members of this marine clade. The predicted ORFs of the IMCC3088 genome also include genes encoding enzymes for the Entner-Doudoroff pathway, the pentose phosphate pathway, ABC transporters for inorganic ions and amino acids, sulfur oxidation (soxCDXYZAB), aromatic compound degradation, and C1 compound metabolism.
Nucleotide sequence accession number.
The genome sequence of strain IMCC3088 is available in GenBank under accession number AEIG00000000.
Acknowledgments
This study was supported by the 21C Frontier Program of Microbial Genomics and Applications and by the Korea Research Foundation Grant funded by the Korean Government (MEST, KRF-2008-521-C00263).
Footnotes
Published ahead of print on 6 May 2011.
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