Application of a Novel <Emphasis Type="Italic">rpoC1</Emphasis>-RFLP Approach Reveals that Marine <Emphasis Type="Italic">Prochlorococcus</Emphasis> Populations in the Atlantic Gyres are Composed of Greater Microdiversity than Previously Described |
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Authors: | Eleanor Jameson Ian Joint Nicholas H Mann Martin Mühling |
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Institution: | (1) Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK;(2) Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK |
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Abstract: | To elucidate the degree of microdiversity within the genus Prochlorococcus, novel Prochlorococcus-specific polymerase chain reaction (PCR) primers were developed for the rpoC1 gene, which encodes the ribonucleic acid (RNA) polymerase core subunit. The size of the PCR fragment (925 bp) coupled with
high sequence variation within the rpoC1 fragments (70–99% sequence similarity, 16S ribosomal RNA sequences show greater than 97% sequence similarity) meant that
it was possible to distinguish Prochlorococcus strains by restriction fragment length polymorphism (RFLP) analysis. Clone libraries were constructed from environmental
deoxyribonucleic acid samples from two stations, one in the northern and one in the southern oligotrophic gyre of the Atlantic
Ocean. These were screened to determine the microdiversity of Prochlorococcus populations using this high-resolution high-throughput analysis approach. RFLP analysis of the clone libraries from the two
gyre sites revealed that the two Prochlorococcus populations had a high degree of microdiversity with 40 and 52 different RFLP-type clones among the 143 clones tested for
both the northern and southern gyres, respectively. Phylogenetic analysis of the nucleotide sequences of the RFLP types not
only showed that it contained representatives of each of the currently recognized Prochlorococcus clades (based on the internal transcribed spacer region as molecular marker) but also led to the discovery of a previously
unseen genetic microdiversity. This level of diversity was greater at the southern gyre site compared to the northern gyre
site. Moreover, the high genetic resolution approach also revealed that there are two putative novel lineages within the HL
I clade. Analyses of further samples by producing clone libraries from different geographic origins is likely to reveal further
diversity and novel lineages within Prochlorococcus. |
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