Browsing by Author "Ulloa, Osvaldo"

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    Diversity 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, Osvaldo
    In 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.
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    Do phytoplankton require oxygen to survive? A hypothesis and model synthesis from oxygen minimum zones
    (2023) Wong, Jane C. Y.; Raven, John A.; Aldunate, Montserrat; Silva, Sebastian; Gaitan-Espitia, Juan Diego; Vargas, Cristian A.; Ulloa, Osvaldo; von Dassow, Peter
    It is commonly known that phytoplankton have a pivotal role in marine biogeochemistry and ecosystems as carbon fixers and oxygen producers, but their response to deoxygenation has scarcely been studied. Nonetheless, in the major oceanic oxygen minimum zones (OMZs), all surface phytoplankton groups, regardless of size, disappear and are replaced by unique cyanobacteria lineages below the oxycline. To develop reasonable hypotheses to explain this pattern, we conduct a review of available information on OMZ phytoplankton, and we re-analyze previously published data (flow cytometric and hydrographic) on vertical structure of phytoplankton communities in relation to light and O-2 levels. We also review the physical constraints on O-2 acquisition as well as O-2-dependent metabolisms in phototrophs. These considerations, along with estimates of the photosynthetic capacity of phytoplankton along OMZ depth profiles using published data, suggest that top-down grazing, respiratory demand, and irradiance are insufficient to fully explain the vertical structure observed in the upper, more sunlit portions of OMZs. Photorespiration and water-water cycles are O-2-dependent pathways with low O-2 affinities. Although their metabolic roles are still poorly understood, a hypothetical dependence on such pathways by the phytoplankton adapted to the oxic ocean might explain vertical patterns in OMZs and results of laboratory experiments. This can be represented in a simple model in which the requirement for photorespiration in surface phytoplankton and O-2-inhibition of OMZ lineages reproduces the observed vertical fluorescence profiles and the replacement of phytoplankton adapted to O-2 by lineages restricted to the most O-2-deficient waters. A high O-2 requirement by modern phytoplankton would suggest a positive feedback that intensifies trends in OMZ extent and ocean oxygenation or deoxygenation, both in Earth's past and in response to current climate change.
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    Novel 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, Osvaldo
    P>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.