Genomic Islands and the Ecology and Evolution of
            <i>Prochlorococcus</i>

Coleman, Maureen L.; Sullivan, Matthew B.; Martiny, Adam C.; Steglich, Claudia; Barry, Kerrie; DeLong, Edward F.; Chisholm, Sallie W.

doi:10.1126/science.1122050

Cited by 410 publications

(442 citation statements)

References 23 publications

Supporting

Mentioning

412

Contrasting

Unclassified

Order By: Relevance

“…The variable region HVR2 provides evidence in support of the hypothesis of bacterial promiscuity (Coleman et al, 2006;Fraser et al, 2007, Vergin et al, 2007. In particular, this study demonstrates the presence of genes within the HVR2 region, which are not present in the genome of 'Cand.…”

Section: Recent Analysis Of the Sargasso Sea And Globalsupporting

confidence: 52%

A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome

2008

View full text Add to dashboard Cite

A sequence analysis is described of a fosmid clone from a coastal marine metagenomic library that contains a 16S rRNA gene with high sequence similarity to that of the SAR11 bacterium 'Candidatus Pelagibacter ubique' HTCC1062. The sequence of the fosmid clone was 32 086 bp in length and contained 23 187 bp of the 48-kb hyper-variable region 2 (HVR2) present in the genome of 'Cand. P. ubique'. However, half of the sequences within the HVR2 region of the fosmid clone show little sequence similarity to or have no representative homologues in the genome sequence of 'Cand. P. ubique' HTCC1062. Given their putative functions, the acquisition of these genes suggests that SAR11 could harbour more diverse phenotypes than represented by the 16S rRNA taxonomy. Variation in SAR11 genomes from different locations might explain why SAR11 is abundant in so many diverse marine provinces.

show abstract

Section: Recent Analysis Of the Sargasso Sea And Globalsupporting

confidence: 52%

A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome

2008

View full text Add to dashboard Cite

show abstract

“…The phylogeny of the proteorhodopsin genes generally matched the topology of the species tree (Supplementary Figure S14) and these loci showed modest recruitment in many of the samples for both strains (Supplementary Table S1), indicating that the subclade Ic may cycle to the euphotic zone with enough frequency, as a population, for the physiological benefits of retaining proteorhodopsin to be realized. Many of the unique or unexpected SAG genes with annotations were located in hypervariable regions (genomic islands), where there was little or no recruitment of metagenomic sequences (Coleman, 2006;Wilhelm et al, 2007;Tully et al, 2011;Grote et al, 2012;Supplementary Table S1). AAA240-E13 and AAA288-E13 had copies of predicted flagellar proteins, including a motor switch protein and a basal-body P-ring protein located together, and AAA240-E13 additionally had a putative flagellar biosynthesis/type III secretory pathway protein.…”

Section: )mentioning

confidence: 99%

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

et al. 2014

View full text Add to dashboard Cite

Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.

show abstract

“…It has been well established that genomic plasticity of microbes, reflected by variations in gene content of closely related strains, may facilitate microbial adaptation to their natural habitats (Coleman et al, 2006;Cuadros-Orellana et al, 2007). We compared the genome sequences of two Pelagibacter coastal isolates (strains HTCC1062 and HTCC1002) and the open ocean isolate (HTCC7211, used as reference genome in the genome-centric analysis above), and asked which HTCC7211-specific genes might be highly expressed and thus functionally important in the open ocean environment.…”

Section: Htcc7211-specific Genesmentioning

confidence: 99%

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

et al. 2010

View full text Add to dashboard Cite

As part of an ongoing survey of microbial community gene expression in the ocean, we sequenced and compared B38 Mbp of community transcriptomes and B157 Mbp of community genomes from four bacterioplankton samples, along a defined depth profile at Station ALOHA in North Pacific subtropical gyre (NPSG). Taxonomic analysis suggested that the samples were dominated by three taxa: Prochlorales, Consistiales and Cenarchaeales, which comprised 36-69% and 29-63% of the annotated sequences in the four DNA and four cDNA libraries, respectively. The relative abundance of these taxonomic groups was sometimes very different in the DNA and cDNA libraries, suggesting differential relative transcriptional activities per cell. For example, the 125 m sample genomic library was dominated by Pelagibacter (B36% of sequence reads), which contributed fewer sequences to the community transcriptome (B11%). Functional characterization of highly expressed genes suggested taxon-specific contributions to specific biogeochemical processes. Examples included Roseobacter relatives involved in aerobic anoxygenic phototrophy at 75 m, and an unexpected contribution of low abundance Crenarchaea to ammonia oxidation at 125 m. Read recruitment using reference microbial genomes indicated depth-specific partitioning of coexisting microbial populations, highlighted by a transcriptionally active high-light-like Prochlorococcus population in the bottom of the photic zone. Additionally, nutrient-uptake genes dominated Pelagibacter transcripts, with apparent enrichment for certain transporter types (for example, the C4-dicarboxylate transport system) over others (for example, phosphate transporters). In total, the data support the utility of coupled DNA and cDNA analyses for describing taxonomic and functional attributes of microbial communities in their natural habitats.

show abstract

Genomic Islands and the Ecology and Evolution of Prochlorococcus

Cited by 410 publications

References 23 publications

A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome

A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

Contact Info

Product

Resources

About