Browsing by Author "Lavin, Paris"
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- ItemDiversity of the marine picocyanobacteria Prochlorococcus and Synechococcus assessed by terminal restriction fragment length polymorphisms of 16S-23S rRNA internal transcribed spacer sequences(2008) Lavin, Paris; Gomez, Patricia; Gonzalez, Bernardo; Ulloa, OsvaldoIn order to assess the appropriateness of the use of internal transcribed spacer (ITS) sequences for the study of population genetics of marine cyanobacteria, we amplified and cloned the 16S rRNA gene plus the 16S-23S ITS regions of six strains of Prochlorococcus and Synechococcus. We analyzed them by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphisms (T-RFLP). When using the standard application of these techniques, We obtained more than one band or terminal restriction fragment (T-RF) per strain or cloned sequence. Reports in literature have Suggested that these anomalies can result from the formation of secondary structures. Secondary structures of the ITS sequences of Prochlorococcus and Synechococcus strains were computationally modelled at the different temperatures that were used during the polymerase chain reaction (PCR). Modelling results predicted the existence of hairpin loops that would still be present at the extension temperature; it is likely that these loops produced incomplete and single stranded PCR products. We modified the standard T-RFLP procedure by adding the labelled ITS primer in the last two cycles of the PCR reaction: this resulted, in most cases, in only one T-RF per ribotype. Application of this technique to a natural picoplankton community in marine waters off northern Chile, showed that it was possible to identify the presence, and determine the relative abundance, of several phylogenetic lineages within the genera Prochlorococcus and Synechococcus inhabiting the euphotic zone. Phylogenetic analysis of ITS sequences obtained by cloning and sequencing DNA from the same sample confirmed the presence of the different genotypes. With the proposed modification, T-RFLP profiles should therefore be Suitable for studying the diversity of natural populations of cyanobacteria, and should become an important tool to study the factors influencing the genetic Structure and distribution of these organisms.
- ItemNovel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific(2010) Lavin, Paris; Gonzalez, Bernardo; Francisco Santibanez, J.; Scanlan, David J.; Ulloa, OsvaldoP>The eastern tropical Pacific Ocean holds two of the main oceanic oxygen minimum zones of the global ocean. The presence of an oxygen-depleted layer at intermediate depths, which also impinges on the seafloor and in some cases the euphotic zone, plays a significant role in structuring both pelagic and benthic communities, and also in the vertical partitioning of microbial assemblages. Here, we assessed the genetic diversity and distribution of natural populations of the cyanobacteria Prochlorococcus and Synechococcus within oxic and suboxic waters of the eastern tropical Pacific using cloning and sequencing, and terminal restriction fragment length polymorphism (T-RFLP) analyses applied to the 16S-23S rRNA internal transcribed spacer region. With the T-RFLP approach we could discriminate 19 cyanobacterial clades, of which 18 were present in the study region. Synechococcus was more abundant in the surface oxic waters of the eastern South Pacific, while Prochlorococcus dominated the subsurface low-oxygen waters. Two of the dominant clades in the oxygen-deficient waters belong to novel and yet uncultivated lineages of low-light adapted Prochlorococcus.
- ItemShort timescale dynamics of phytoplankton in Fildes Bay, Antarctica.(2017) Egas, Claudia; Henríquez Castillo, Carlos Andrés; Delherbe, Nathalie; Molina, Ernesto; Dos Santos, Adriana; Lavin, Paris; De la Iglesia Cabezas, Rodrigo Alonso; Vaulot, Daniel; Trefault Carrillo, Nicole Natalie