Article

Complete genome sequence of strain IMCC9063, belonging to SAR11 subgroup 3, isolated from the Arctic Ocean.

Division of Biology and Ocean Sciences, Inha University, Incheon, Republic of Korea.
Journal of bacteriology (impact factor: 3.94). 07/2011; 193(13):3379-80. DOI:10.1128/JB.05033-11 pp.3379-80
Source: PubMed

ABSTRACT Strain IMCC9063 is a novel isolate of the SAR11 clade and is distantly related to other cultured representatives in this clade. The strain was isolated off the coast of Svalbard, Norway, by applying high-throughput culturing methods based on dilution to extinction. Here we present the finished genome sequence of strain IMCC9063.

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    Article: Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea.
    David Kamanda Ngugi, Ulrich Stingl
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    ABSTRACT: Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24°C throughout the year, and a remarkable uniform temperature (∼22°C) and salinity (∼41 psu) from the mixed layer (∼200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea's water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.
    PLoS ONE 01/2012; 7(11):e50274. · 4.09 Impact Factor
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Keywords

clade
 
cultured representatives
 
dilution
 
finished genome sequence
 
Norway
 
SAR11 clade
 

Hyun-Myung Oh