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Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum.

Wang H, Tomasch J, Michael V, Bhuju S, Jarek M, Petersen J, Wagner-Döbler I - Front Microbiol (2015)

Bottom Line: Here, we identified key genetic components of this interaction.By contrast, pathogenicity was entirely dependent on one of the extrachromosomal elements of D. shibae, the 191 kb plasmid.The data show that flagella and the CtrA phosphorelay are required for establishing mutualism and prove a cell density dependent killing effect of D. shibae on P. minimum which is mediated by an unknown factor encoded on the 191 kb plasmid.

View Article: PubMed Central - PubMed

Affiliation: Helmholtz-Centre for Infection Research, Microbial Communication Braunschweig, Germany.

ABSTRACT
The co-cultivation of the alphaproteobacterium Dinoroseobacter shibae with the dinoflagellate Prorocentrum minimum is characterized by a mutualistic phase followed by a pathogenic phase in which the bacterium kills aging algae. Thus it resembles the "Jekyll-and-Hyde" interaction that has been proposed for other algae and Roseobacter. Here, we identified key genetic components of this interaction. Analysis of the transcriptome of D. shibae in co-culture with P. minimum revealed growth phase dependent changes in the expression of quorum sensing, the CtrA phosphorelay, and flagella biosynthesis genes. Deletion of the histidine kinase gene cckA which is part of the CtrA phosphorelay or the flagella genes fliC or flgK resulted in complete lack of growth stimulation of P. minimum in co-culture with the D. shibae mutants. By contrast, pathogenicity was entirely dependent on one of the extrachromosomal elements of D. shibae, the 191 kb plasmid. The data show that flagella and the CtrA phosphorelay are required for establishing mutualism and prove a cell density dependent killing effect of D. shibae on P. minimum which is mediated by an unknown factor encoded on the 191 kb plasmid.

No MeSH data available.


Related in: MedlinePlus

Growth of P. minimum and D. shibae in co-culture. In the mutualistic phase (day 0–day 21) both organisms profit from the co-cultivation in a medium where the dinoflagellate and the bacterium are not able to grow in single culture due to lack of vitamin B12 and organic carbon, respectively. In the pathogenic phase (day 21–day 36) the algae are killed by the bacteria, which continue to grow. Red arrows indicate the sampling time points for transcriptome analysis (modified from Wang et al., 2014a).
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Figure 1: Growth of P. minimum and D. shibae in co-culture. In the mutualistic phase (day 0–day 21) both organisms profit from the co-cultivation in a medium where the dinoflagellate and the bacterium are not able to grow in single culture due to lack of vitamin B12 and organic carbon, respectively. In the pathogenic phase (day 21–day 36) the algae are killed by the bacteria, which continue to grow. Red arrows indicate the sampling time points for transcriptome analysis (modified from Wang et al., 2014a).

Mentions: In our previous work we demonstrated that population dynamics of P. minimum in the co-culture with D. shibae exhibited a mutualistic phase (day 1 to day 21) where both partners profit from each other and a pathogenic phase (day 21 to day 36) where D. shibae kills aging dinoflagellate cells (Wang et al., 2014a). In the same study we analyzed the influence of light on the transcriptome of D. shibae at an early stage (day 12) of the co-cultivation (Wang et al., 2014a). Here, we used RNA-sequencing of samples from the same co-cultivation experiment to analyze the transcriptome of D. shibae at three different growth stages: (1) day 18 when D. shibae was in the mid-exponential growth phase, while P. minimum had entered the stationary phase; (2) day 24 when D. shibae had entered the stationary phase, while P. minimum started to decline; (3) day 30 when P. minimum had almost vanished, while D. shibae remained in the stationary phase (Figure 1). Two of the three biological replicate samples for each time point were used for RNA-seq analysis. The library sizes of the samples from different time-points increased with the increasing density of bacteria in the co-culture. Samples from day 18 reached only 15 and 139 k unique mapping reads, while samples from later time-points reached more than one to five million unique mapping reads (Supplementary Table S1). Despite these differences in sequencing depth the correlation between replicates was satisfactory for all time-points (Supplementary Figure S1A). To determine a cut-off for reliable changes in gene expression we reduced the sequencing depth for day 24 and day 30 to 100 k reads by resampling. The deviation in expression and log2 fold-change between the reduced and original dataset strongly increased for genes with an abundance of log2 cpm (counts per gene per million reads) lower than seven. We defined this value as the lower cut-off for reliable gene expression at day 18 (Supplementary Figures S1B,C). Only four of the 41 genes identified as significantly differentially expressed had a cpm-value slightly below this cut-off and therefor have to be treated with caution. This is consistent with our previous study, showing that small library sizes increase the error of the obtained reads per gene in particular for weakly expressed genes (Wang et al., 2014a).


Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum.

Wang H, Tomasch J, Michael V, Bhuju S, Jarek M, Petersen J, Wagner-Döbler I - Front Microbiol (2015)

Growth of P. minimum and D. shibae in co-culture. In the mutualistic phase (day 0–day 21) both organisms profit from the co-cultivation in a medium where the dinoflagellate and the bacterium are not able to grow in single culture due to lack of vitamin B12 and organic carbon, respectively. In the pathogenic phase (day 21–day 36) the algae are killed by the bacteria, which continue to grow. Red arrows indicate the sampling time points for transcriptome analysis (modified from Wang et al., 2014a).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4643747&req=5

Figure 1: Growth of P. minimum and D. shibae in co-culture. In the mutualistic phase (day 0–day 21) both organisms profit from the co-cultivation in a medium where the dinoflagellate and the bacterium are not able to grow in single culture due to lack of vitamin B12 and organic carbon, respectively. In the pathogenic phase (day 21–day 36) the algae are killed by the bacteria, which continue to grow. Red arrows indicate the sampling time points for transcriptome analysis (modified from Wang et al., 2014a).
Mentions: In our previous work we demonstrated that population dynamics of P. minimum in the co-culture with D. shibae exhibited a mutualistic phase (day 1 to day 21) where both partners profit from each other and a pathogenic phase (day 21 to day 36) where D. shibae kills aging dinoflagellate cells (Wang et al., 2014a). In the same study we analyzed the influence of light on the transcriptome of D. shibae at an early stage (day 12) of the co-cultivation (Wang et al., 2014a). Here, we used RNA-sequencing of samples from the same co-cultivation experiment to analyze the transcriptome of D. shibae at three different growth stages: (1) day 18 when D. shibae was in the mid-exponential growth phase, while P. minimum had entered the stationary phase; (2) day 24 when D. shibae had entered the stationary phase, while P. minimum started to decline; (3) day 30 when P. minimum had almost vanished, while D. shibae remained in the stationary phase (Figure 1). Two of the three biological replicate samples for each time point were used for RNA-seq analysis. The library sizes of the samples from different time-points increased with the increasing density of bacteria in the co-culture. Samples from day 18 reached only 15 and 139 k unique mapping reads, while samples from later time-points reached more than one to five million unique mapping reads (Supplementary Table S1). Despite these differences in sequencing depth the correlation between replicates was satisfactory for all time-points (Supplementary Figure S1A). To determine a cut-off for reliable changes in gene expression we reduced the sequencing depth for day 24 and day 30 to 100 k reads by resampling. The deviation in expression and log2 fold-change between the reduced and original dataset strongly increased for genes with an abundance of log2 cpm (counts per gene per million reads) lower than seven. We defined this value as the lower cut-off for reliable gene expression at day 18 (Supplementary Figures S1B,C). Only four of the 41 genes identified as significantly differentially expressed had a cpm-value slightly below this cut-off and therefor have to be treated with caution. This is consistent with our previous study, showing that small library sizes increase the error of the obtained reads per gene in particular for weakly expressed genes (Wang et al., 2014a).

Bottom Line: Here, we identified key genetic components of this interaction.By contrast, pathogenicity was entirely dependent on one of the extrachromosomal elements of D. shibae, the 191 kb plasmid.The data show that flagella and the CtrA phosphorelay are required for establishing mutualism and prove a cell density dependent killing effect of D. shibae on P. minimum which is mediated by an unknown factor encoded on the 191 kb plasmid.

View Article: PubMed Central - PubMed

Affiliation: Helmholtz-Centre for Infection Research, Microbial Communication Braunschweig, Germany.

ABSTRACT
The co-cultivation of the alphaproteobacterium Dinoroseobacter shibae with the dinoflagellate Prorocentrum minimum is characterized by a mutualistic phase followed by a pathogenic phase in which the bacterium kills aging algae. Thus it resembles the "Jekyll-and-Hyde" interaction that has been proposed for other algae and Roseobacter. Here, we identified key genetic components of this interaction. Analysis of the transcriptome of D. shibae in co-culture with P. minimum revealed growth phase dependent changes in the expression of quorum sensing, the CtrA phosphorelay, and flagella biosynthesis genes. Deletion of the histidine kinase gene cckA which is part of the CtrA phosphorelay or the flagella genes fliC or flgK resulted in complete lack of growth stimulation of P. minimum in co-culture with the D. shibae mutants. By contrast, pathogenicity was entirely dependent on one of the extrachromosomal elements of D. shibae, the 191 kb plasmid. The data show that flagella and the CtrA phosphorelay are required for establishing mutualism and prove a cell density dependent killing effect of D. shibae on P. minimum which is mediated by an unknown factor encoded on the 191 kb plasmid.

No MeSH data available.


Related in: MedlinePlus