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De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms.

Frischkorn KR, Harke MJ, Gobler CJ, Dyhrman ST - Front Microbiol (2014)

Bottom Line: On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods.A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains.These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University Palisades, NY, USA.

ABSTRACT
Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte Aureococcus anophagefferens strain CCMP 1850 to assess responses to common stressors for dense phytoplankton blooms: low inorganic nitrogen concentrations, low inorganic phosphorus concentrations, low light levels, and a replete control. The de novo assemblies of pooled reads from all treatments reconstructed ~54,000 transcripts using Trinity, and ~31,000 transcripts using ABySS. Comparison to the strain CCMP 1984 genome showed that the majority of the gene models were present in both de novo assemblies and that roughly 95% of contigs from both assemblies mapped to the genome, with Trinity capturing slightly more genome content. Sequence reads were mapped back to the de novo assemblies as well as the gene models and differential expression was analyzed using a Bayesian approach called Analysis of Sequence Counts (ASC). On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods. Transcripts related to the transport and metabolism of nitrogen were upregulated in the low nitrogen treatment, transcripts encoding enzymes that hydrolyze organic phosphorus or relieve arsenic toxicity were upregulated in the low phosphorus treatment, and transcripts for enzymes that catabolize organic compounds, restructure lipid membranes, or are involved in sulfolipid biosynthesis were upregulated in the low light treatment. A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains. These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

No MeSH data available.


Related in: MedlinePlus

Cell growth in each treatment. Error bars represent standard deviation of triplicate cultures. Arrows indicate time of harvest.
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Figure 1: Cell growth in each treatment. Error bars represent standard deviation of triplicate cultures. Arrows indicate time of harvest.

Mentions: The replete cultures were harvested during the exponential phase of growth on day 9 (Figure 1). The low nutrient cultures were harvested in early stationary phase; this corresponded to day 9 in low N and day 12 in low P. The cultures grown in low light maintained a steady low growth rate and were harvested on day 9 (Figure 1). At the time of harvest, control cultures were growing at significantly higher rates (0.49 d−1) than those of the treatments, which ranged from 0.01 to 0.09 d−1 (p < 0.001). The longer lag time in replete and low P cultures relative to low N is likely due to the initial excess of ammonium hindering growth, which has been seen in similar studies (Wurch et al., 2014). In the low N and low P cultures, the reduced growth rates were consistent with reduced concentrations of N or P, respectively (Table 1). Inorganic phosphate concentrations in the low P treatment at the time of harvest were 1.34 ± 0.23 μM and were significantly lower than the other treatments (>3 μM; p < 0.001). Nitrate levels were below the detection limit in the low N treatment but were >9 μM in the replete, low P and low light treatments. Ammonium levels in the low N treatment were also significantly lower (1.76 ± 0.28 μM) than the other three treatments (13–38 μM; p < 0.001). Photosynthetic efficiency of photosystem II (Fv/Fm) at the time of harvest was significantly higher in the control (0.58 ± 0.02; p < 0.05) than all other treatments (Table 1). The APA was measured during stationary phase and just prior to harvesting (days 10 and 11) in the low P cultures, and on days 6 and 7 during exponential phase in the replete condition cultures (Figure 1). The average activity in the triplicate cultures over the 2 days prior to harvesting was 4.0 nmol P L−1 h−1 in the low P treatment and 2.1 nmol P L−1 h−1 in the replete cultures.


De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms.

Frischkorn KR, Harke MJ, Gobler CJ, Dyhrman ST - Front Microbiol (2014)

Cell growth in each treatment. Error bars represent standard deviation of triplicate cultures. Arrows indicate time of harvest.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109616&req=5

Figure 1: Cell growth in each treatment. Error bars represent standard deviation of triplicate cultures. Arrows indicate time of harvest.
Mentions: The replete cultures were harvested during the exponential phase of growth on day 9 (Figure 1). The low nutrient cultures were harvested in early stationary phase; this corresponded to day 9 in low N and day 12 in low P. The cultures grown in low light maintained a steady low growth rate and were harvested on day 9 (Figure 1). At the time of harvest, control cultures were growing at significantly higher rates (0.49 d−1) than those of the treatments, which ranged from 0.01 to 0.09 d−1 (p < 0.001). The longer lag time in replete and low P cultures relative to low N is likely due to the initial excess of ammonium hindering growth, which has been seen in similar studies (Wurch et al., 2014). In the low N and low P cultures, the reduced growth rates were consistent with reduced concentrations of N or P, respectively (Table 1). Inorganic phosphate concentrations in the low P treatment at the time of harvest were 1.34 ± 0.23 μM and were significantly lower than the other treatments (>3 μM; p < 0.001). Nitrate levels were below the detection limit in the low N treatment but were >9 μM in the replete, low P and low light treatments. Ammonium levels in the low N treatment were also significantly lower (1.76 ± 0.28 μM) than the other three treatments (13–38 μM; p < 0.001). Photosynthetic efficiency of photosystem II (Fv/Fm) at the time of harvest was significantly higher in the control (0.58 ± 0.02; p < 0.05) than all other treatments (Table 1). The APA was measured during stationary phase and just prior to harvesting (days 10 and 11) in the low P cultures, and on days 6 and 7 during exponential phase in the replete condition cultures (Figure 1). The average activity in the triplicate cultures over the 2 days prior to harvesting was 4.0 nmol P L−1 h−1 in the low P treatment and 2.1 nmol P L−1 h−1 in the replete cultures.

Bottom Line: On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods.A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains.These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University Palisades, NY, USA.

ABSTRACT
Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte Aureococcus anophagefferens strain CCMP 1850 to assess responses to common stressors for dense phytoplankton blooms: low inorganic nitrogen concentrations, low inorganic phosphorus concentrations, low light levels, and a replete control. The de novo assemblies of pooled reads from all treatments reconstructed ~54,000 transcripts using Trinity, and ~31,000 transcripts using ABySS. Comparison to the strain CCMP 1984 genome showed that the majority of the gene models were present in both de novo assemblies and that roughly 95% of contigs from both assemblies mapped to the genome, with Trinity capturing slightly more genome content. Sequence reads were mapped back to the de novo assemblies as well as the gene models and differential expression was analyzed using a Bayesian approach called Analysis of Sequence Counts (ASC). On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods. Transcripts related to the transport and metabolism of nitrogen were upregulated in the low nitrogen treatment, transcripts encoding enzymes that hydrolyze organic phosphorus or relieve arsenic toxicity were upregulated in the low phosphorus treatment, and transcripts for enzymes that catabolize organic compounds, restructure lipid membranes, or are involved in sulfolipid biosynthesis were upregulated in the low light treatment. A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains. These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

No MeSH data available.


Related in: MedlinePlus