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Clade-Specific Quantitative Analysis of Photosynthetic Gene Expression in Prochlorococcus.

Fernández-Pinos MC, Casado M, Caballero G, Zinser ER, Dachs J, Piña B - PLoS ONE (2015)

Bottom Line: After optimizing sample collection methodology, we analyzed a total of 62 stations from the Malaspina 2010 circumnavigation (including Atlantic, Pacific and Indian Oceans) at three different depths.Sequence and quantitative analyses of the corresponding amplicons showed the presence of high-light (HL) and low-light (LL) Prochlorococcus clades in essentially all 182 samples, with a largely uniform stratification of LL and HL sequences.Synechococcus cross-amplifications were detected by the taxon-specific melting temperatures of the amplicons.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalonia, Spain.

ABSTRACT
Newly designed primers targeting rbcL (CO2 fixation), psbA (photosystem II) and rnpB (reference) genes were used in qRT-PCR assays to assess the photosynthetic capability of natural communities of Prochlorococcus, the most abundant photosynthetic organism on Earth and a major contributor to primary production in oligotrophic oceans. After optimizing sample collection methodology, we analyzed a total of 62 stations from the Malaspina 2010 circumnavigation (including Atlantic, Pacific and Indian Oceans) at three different depths. Sequence and quantitative analyses of the corresponding amplicons showed the presence of high-light (HL) and low-light (LL) Prochlorococcus clades in essentially all 182 samples, with a largely uniform stratification of LL and HL sequences. Synechococcus cross-amplifications were detected by the taxon-specific melting temperatures of the amplicons. Laboratory exposure of Prochlorococcus MED4 (HL) and MIT9313 (LL) strains to organic pollutants (PAHs and organochlorine compounds) showed a decrease of rbcL transcript abundances, and of the rbcL to psbA ratios for both strains. We propose this technique as a convenient assay to evaluate effects of environmental stressors, including pollution, on the oceanic Prochlorococcus photosynthetic function.

No MeSH data available.


Related in: MedlinePlus

Relative expression of rbcL and psbA in surface (orange), DCM (green) and DCM+40 m (blue) samples for HL (left) and LL (right) clades.The boxes indicate data distribution parameters: range (whiskers), 25 to 75 percentiles (boxes) and median (thick horizontal bar). Circles represent outliers. Letters indicate statistically different distribution (ANOVA plus SD Tukey post hoc test); the corresponding p values are indicated at the bottom.
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pone.0133207.g002: Relative expression of rbcL and psbA in surface (orange), DCM (green) and DCM+40 m (blue) samples for HL (left) and LL (right) clades.The boxes indicate data distribution parameters: range (whiskers), 25 to 75 percentiles (boxes) and median (thick horizontal bar). Circles represent outliers. Letters indicate statistically different distribution (ANOVA plus SD Tukey post hoc test); the corresponding p values are indicated at the bottom.

Mentions: Fig 2 shows the global distributions of relative abundances of rbcL and psbA, normalized by the reference gene rnpB, for the two clades and at the three sampled depths. The relative mRNA abundances of both HL genes decreased with the depth, being maximal at 3 m depth and minimal at DCM+40. On average, 3 m depth samples showed five times more HL rbcL, and three times more HL psbA mRNA copies than DCM+40 samples (Fig 2). LL genes showed the opposite tendency, although the effect was less clear. LL rbcL mRNA was about three times more abundant at DCM, or DCM+40, than at 3 m depth samples, whereas no significant differences were observed for LL psbA, in part due to the high dispersion of the values at 3 m depth (Table 4).


Clade-Specific Quantitative Analysis of Photosynthetic Gene Expression in Prochlorococcus.

Fernández-Pinos MC, Casado M, Caballero G, Zinser ER, Dachs J, Piña B - PLoS ONE (2015)

Relative expression of rbcL and psbA in surface (orange), DCM (green) and DCM+40 m (blue) samples for HL (left) and LL (right) clades.The boxes indicate data distribution parameters: range (whiskers), 25 to 75 percentiles (boxes) and median (thick horizontal bar). Circles represent outliers. Letters indicate statistically different distribution (ANOVA plus SD Tukey post hoc test); the corresponding p values are indicated at the bottom.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526520&req=5

pone.0133207.g002: Relative expression of rbcL and psbA in surface (orange), DCM (green) and DCM+40 m (blue) samples for HL (left) and LL (right) clades.The boxes indicate data distribution parameters: range (whiskers), 25 to 75 percentiles (boxes) and median (thick horizontal bar). Circles represent outliers. Letters indicate statistically different distribution (ANOVA plus SD Tukey post hoc test); the corresponding p values are indicated at the bottom.
Mentions: Fig 2 shows the global distributions of relative abundances of rbcL and psbA, normalized by the reference gene rnpB, for the two clades and at the three sampled depths. The relative mRNA abundances of both HL genes decreased with the depth, being maximal at 3 m depth and minimal at DCM+40. On average, 3 m depth samples showed five times more HL rbcL, and three times more HL psbA mRNA copies than DCM+40 samples (Fig 2). LL genes showed the opposite tendency, although the effect was less clear. LL rbcL mRNA was about three times more abundant at DCM, or DCM+40, than at 3 m depth samples, whereas no significant differences were observed for LL psbA, in part due to the high dispersion of the values at 3 m depth (Table 4).

Bottom Line: After optimizing sample collection methodology, we analyzed a total of 62 stations from the Malaspina 2010 circumnavigation (including Atlantic, Pacific and Indian Oceans) at three different depths.Sequence and quantitative analyses of the corresponding amplicons showed the presence of high-light (HL) and low-light (LL) Prochlorococcus clades in essentially all 182 samples, with a largely uniform stratification of LL and HL sequences.Synechococcus cross-amplifications were detected by the taxon-specific melting temperatures of the amplicons.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalonia, Spain.

ABSTRACT
Newly designed primers targeting rbcL (CO2 fixation), psbA (photosystem II) and rnpB (reference) genes were used in qRT-PCR assays to assess the photosynthetic capability of natural communities of Prochlorococcus, the most abundant photosynthetic organism on Earth and a major contributor to primary production in oligotrophic oceans. After optimizing sample collection methodology, we analyzed a total of 62 stations from the Malaspina 2010 circumnavigation (including Atlantic, Pacific and Indian Oceans) at three different depths. Sequence and quantitative analyses of the corresponding amplicons showed the presence of high-light (HL) and low-light (LL) Prochlorococcus clades in essentially all 182 samples, with a largely uniform stratification of LL and HL sequences. Synechococcus cross-amplifications were detected by the taxon-specific melting temperatures of the amplicons. Laboratory exposure of Prochlorococcus MED4 (HL) and MIT9313 (LL) strains to organic pollutants (PAHs and organochlorine compounds) showed a decrease of rbcL transcript abundances, and of the rbcL to psbA ratios for both strains. We propose this technique as a convenient assay to evaluate effects of environmental stressors, including pollution, on the oceanic Prochlorococcus photosynthetic function.

No MeSH data available.


Related in: MedlinePlus