Limits...
Gene expression in the mixotrophic prymnesiophyte, Prymnesium parvum, responds to prey availability.

Liu Z, Jones AC, Campbell V, Hambright KD, Heidelberg KB, Caron DA - Front Microbiol (2015)

Bottom Line: It produces toxins and can form ecosystem disruptive blooms that result in fish kills and changes in planktonic food web structure.However, both transcriptomic data and growth experiments indicated that P. parvum did not grow faster in the presence of prey despite the gains in nutrients, although algal abundances attained in culture were slightly greater in the presence of prey.The relationship between phototrophy, heterotrophy and growth of P. parvum is discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Southern California Los Angeles, CA, USA.

ABSTRACT
The mixotrophic prymnesiophyte, Prymnesium parvum, is a widely distributed alga with significant ecological importance. It produces toxins and can form ecosystem disruptive blooms that result in fish kills and changes in planktonic food web structure. However, the relationship between P. parvum and its prey on the molecular level is poorly understood. In this study, we used RNA-Seq technology to study changes in gene transcription of P. parvum in three treatments with different microbial populations available as potential prey: axenic P. parvum (no prey), bacterized P. paruvm, and axenic P. parvum with ciliates added as prey. Thousands of genes were differentially expressed among the three treatments. Most notably, transcriptome data indicated that P. parvum obtained organic carbon, including fatty acids, from both bacteria and ciliate prey for energy and cellular building blocks. The data also suggested that different prey provided P. parvum with macro- and micro-nutrients, namely organic nitrogen in the form of amino acids from ciliates, and iron from bacteria. However, both transcriptomic data and growth experiments indicated that P. parvum did not grow faster in the presence of prey despite the gains in nutrients, although algal abundances attained in culture were slightly greater in the presence of prey. The relationship between phototrophy, heterotrophy and growth of P. parvum is discussed.

No MeSH data available.


Relative expression levels of individual genes of P. parvum within different metabolic pathways or functions. Each dot represents an individual gene. X-axis values indicate expression levels in bacterized treatment relative to those in axenic treatment (FPKMbacterized/FPKMaxenic). Y-axis values indicate expression levels in ciliate treatment relative to those in axenic treatment (FPKMciliate/FPKMaxenic). Sizes of the dots are proportional to the number of reads assigned to the genes. Not all genes within certain pathways or functions are shown, only those that have differential expression between at least a pair of treatments. These functions and pathways with significantly differential gene expression were plotted in Figures 3–5 to further show consistent patterns within each function/pathway that are highlighted in our discussion of core metabolism of P. parvum. For list of genes and their read counts, FPKM values, and relative expression levels, refer to Table S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4403553&req=5

Figure 3: Relative expression levels of individual genes of P. parvum within different metabolic pathways or functions. Each dot represents an individual gene. X-axis values indicate expression levels in bacterized treatment relative to those in axenic treatment (FPKMbacterized/FPKMaxenic). Y-axis values indicate expression levels in ciliate treatment relative to those in axenic treatment (FPKMciliate/FPKMaxenic). Sizes of the dots are proportional to the number of reads assigned to the genes. Not all genes within certain pathways or functions are shown, only those that have differential expression between at least a pair of treatments. These functions and pathways with significantly differential gene expression were plotted in Figures 3–5 to further show consistent patterns within each function/pathway that are highlighted in our discussion of core metabolism of P. parvum. For list of genes and their read counts, FPKM values, and relative expression levels, refer to Table S2.

Mentions: A more detailed evaluation of differential gene expression and function with respect to roles in P. parvum showed that most (>50%) of its genes had no matches or functional annotations to existing databases, owing to the relative scarcity of protistan sequence data (Caron et al., 2009). Nevertheless, we were able to infer interesting patterns from changes in the transcriptional patterns of those genes with putative functions (Figure 3). Genes belonging to the same pathway or metabolic function had very similar transcriptional patterns among the treatments. For example, all differential expressed genes associated with fatty acid metabolism had higher expression levels in the presence of either prey type and formed a cluster in the upper right quadrant of Figure 3, while genes associated with iron uptake clustered together in the lower left quadrant (i.e., the latter genes had lower expression levels in the presence of both prey). Figure 3 also illustrates that genes associated with different metabolic functions often demonstrated different transcriptional patterns (as noted above). While changes in transcription do not necessarily equate with protein concentrations or enzymatic activities, the transcriptional patterns observed in this study provided insights into the relationship between P. parvum and the presence of potential prey, and different prey types.


Gene expression in the mixotrophic prymnesiophyte, Prymnesium parvum, responds to prey availability.

Liu Z, Jones AC, Campbell V, Hambright KD, Heidelberg KB, Caron DA - Front Microbiol (2015)

Relative expression levels of individual genes of P. parvum within different metabolic pathways or functions. Each dot represents an individual gene. X-axis values indicate expression levels in bacterized treatment relative to those in axenic treatment (FPKMbacterized/FPKMaxenic). Y-axis values indicate expression levels in ciliate treatment relative to those in axenic treatment (FPKMciliate/FPKMaxenic). Sizes of the dots are proportional to the number of reads assigned to the genes. Not all genes within certain pathways or functions are shown, only those that have differential expression between at least a pair of treatments. These functions and pathways with significantly differential gene expression were plotted in Figures 3–5 to further show consistent patterns within each function/pathway that are highlighted in our discussion of core metabolism of P. parvum. For list of genes and their read counts, FPKM values, and relative expression levels, refer to Table S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403553&req=5

Figure 3: Relative expression levels of individual genes of P. parvum within different metabolic pathways or functions. Each dot represents an individual gene. X-axis values indicate expression levels in bacterized treatment relative to those in axenic treatment (FPKMbacterized/FPKMaxenic). Y-axis values indicate expression levels in ciliate treatment relative to those in axenic treatment (FPKMciliate/FPKMaxenic). Sizes of the dots are proportional to the number of reads assigned to the genes. Not all genes within certain pathways or functions are shown, only those that have differential expression between at least a pair of treatments. These functions and pathways with significantly differential gene expression were plotted in Figures 3–5 to further show consistent patterns within each function/pathway that are highlighted in our discussion of core metabolism of P. parvum. For list of genes and their read counts, FPKM values, and relative expression levels, refer to Table S2.
Mentions: A more detailed evaluation of differential gene expression and function with respect to roles in P. parvum showed that most (>50%) of its genes had no matches or functional annotations to existing databases, owing to the relative scarcity of protistan sequence data (Caron et al., 2009). Nevertheless, we were able to infer interesting patterns from changes in the transcriptional patterns of those genes with putative functions (Figure 3). Genes belonging to the same pathway or metabolic function had very similar transcriptional patterns among the treatments. For example, all differential expressed genes associated with fatty acid metabolism had higher expression levels in the presence of either prey type and formed a cluster in the upper right quadrant of Figure 3, while genes associated with iron uptake clustered together in the lower left quadrant (i.e., the latter genes had lower expression levels in the presence of both prey). Figure 3 also illustrates that genes associated with different metabolic functions often demonstrated different transcriptional patterns (as noted above). While changes in transcription do not necessarily equate with protein concentrations or enzymatic activities, the transcriptional patterns observed in this study provided insights into the relationship between P. parvum and the presence of potential prey, and different prey types.

Bottom Line: It produces toxins and can form ecosystem disruptive blooms that result in fish kills and changes in planktonic food web structure.However, both transcriptomic data and growth experiments indicated that P. parvum did not grow faster in the presence of prey despite the gains in nutrients, although algal abundances attained in culture were slightly greater in the presence of prey.The relationship between phototrophy, heterotrophy and growth of P. parvum is discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of Southern California Los Angeles, CA, USA.

ABSTRACT
The mixotrophic prymnesiophyte, Prymnesium parvum, is a widely distributed alga with significant ecological importance. It produces toxins and can form ecosystem disruptive blooms that result in fish kills and changes in planktonic food web structure. However, the relationship between P. parvum and its prey on the molecular level is poorly understood. In this study, we used RNA-Seq technology to study changes in gene transcription of P. parvum in three treatments with different microbial populations available as potential prey: axenic P. parvum (no prey), bacterized P. paruvm, and axenic P. parvum with ciliates added as prey. Thousands of genes were differentially expressed among the three treatments. Most notably, transcriptome data indicated that P. parvum obtained organic carbon, including fatty acids, from both bacteria and ciliate prey for energy and cellular building blocks. The data also suggested that different prey provided P. parvum with macro- and micro-nutrients, namely organic nitrogen in the form of amino acids from ciliates, and iron from bacteria. However, both transcriptomic data and growth experiments indicated that P. parvum did not grow faster in the presence of prey despite the gains in nutrients, although algal abundances attained in culture were slightly greater in the presence of prey. The relationship between phototrophy, heterotrophy and growth of P. parvum is discussed.

No MeSH data available.