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Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.

Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, Daniel R, Simon M, Brinkhoff T - BMC Genomics (2011)

Bottom Line: The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements.Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data.The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.

ABSTRACT

Background: Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis.

Results: The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype.

Conclusions: The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149_94 was probably translocated from the chromosome. Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have a common ancestor and are important for cell envelope biosynthesis. Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data. The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.

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Respiration rates of R. litoralis cells. A: exponential growth phase; B: stationary growth phase. The values in mV min-1 indicate the respiration rates in the respective time intervals. Cells were kept anoxic under nitrogen gas until oxygen was supplied. At the beginning of each respiration measurement the cell suspension was saturated with oxygen and the oxygen consumption of the cells was measured in mV min-1. The response of R. litoralis to light differs remarkably between the two growth phases. During the exponential growth phase the initial respiration rate in the dark was higher (220 mV min-1) than in the stationary growth phase (140 mV min-1). When exposed to light, the cells that were in the exponential growth phase showed only a slight decrease to 200 mV min-1 (10%) of the respiration rate whereas in the stationary phase culture the respiration rate was reduced to 43% (60 mV min-1) of the original rate in the first light period and to 25% (30 mV min-1) in the second. Cells resumed 95% (exponential growth phase) and 86% (stationary growth phase) of their original respiration rate when darkened again.
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Figure 4: Respiration rates of R. litoralis cells. A: exponential growth phase; B: stationary growth phase. The values in mV min-1 indicate the respiration rates in the respective time intervals. Cells were kept anoxic under nitrogen gas until oxygen was supplied. At the beginning of each respiration measurement the cell suspension was saturated with oxygen and the oxygen consumption of the cells was measured in mV min-1. The response of R. litoralis to light differs remarkably between the two growth phases. During the exponential growth phase the initial respiration rate in the dark was higher (220 mV min-1) than in the stationary growth phase (140 mV min-1). When exposed to light, the cells that were in the exponential growth phase showed only a slight decrease to 200 mV min-1 (10%) of the respiration rate whereas in the stationary phase culture the respiration rate was reduced to 43% (60 mV min-1) of the original rate in the first light period and to 25% (30 mV min-1) in the second. Cells resumed 95% (exponential growth phase) and 86% (stationary growth phase) of their original respiration rate when darkened again.

Mentions: To confirm the functionality of the plasmid-encoded photosynthesis apparatus in R. litoralis, the photosynthetic activity of the strain was measured via oxygen consumption (Figure 4). Whereas almost no reaction to light was observed during growth, cells in the stationary growth phase were highly responsive to light and showed a reduced respiration rate when exposed to light (Figure 4). Even though pigmentation occurred already during the exponential growth phase, the organism did not use the photosynthetic apparatus until the culture reached the stationary growth phase. The use, but not the expression, of the photosynthesis apparatus might therefore be influenced by nutrient availability in R. litoralis, as stationary phase cultures are nutrient depleted. We obtained similar results for R. denitrificans, with cells in the late stationary phase showing a stronger response to light than cells from the exponential growth phase (data not shown). For the alpha-Proteobacteria Labrenzia alexandrii DFl-11 and Hoeflea phototrophica DFL-43 periodic nutrient starvation has been reported to trigger bacteriochlorophyll-a production whereas only slight effects were observed for D. shibae [40]. Obviously, the regulation mechanisms differ between the aerobic phototrophic bacteria and so does the architecture of their photosynthesis genes. In Additional File 3, the organization of the photosynthesis gene clusters of the organisms mentioned above is compared, showing that organisms with similar physiological traits also have similar gene organizations. The suggestion that the organization of genes within purple bacterial photosynthesis gene clusters reflects regulatory mechanisms, evolutionary history, and relationships between species was also made by other authors [7,41,42]. In the oligotrophic environment of the ocean, the use of the photosynthesis apparatus during nutrient depletion may be an important advantage for Roseobacter species in the competition with non-photosynthetic organisms.


Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis.

Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, Daniel R, Simon M, Brinkhoff T - BMC Genomics (2011)

Respiration rates of R. litoralis cells. A: exponential growth phase; B: stationary growth phase. The values in mV min-1 indicate the respiration rates in the respective time intervals. Cells were kept anoxic under nitrogen gas until oxygen was supplied. At the beginning of each respiration measurement the cell suspension was saturated with oxygen and the oxygen consumption of the cells was measured in mV min-1. The response of R. litoralis to light differs remarkably between the two growth phases. During the exponential growth phase the initial respiration rate in the dark was higher (220 mV min-1) than in the stationary growth phase (140 mV min-1). When exposed to light, the cells that were in the exponential growth phase showed only a slight decrease to 200 mV min-1 (10%) of the respiration rate whereas in the stationary phase culture the respiration rate was reduced to 43% (60 mV min-1) of the original rate in the first light period and to 25% (30 mV min-1) in the second. Cells resumed 95% (exponential growth phase) and 86% (stationary growth phase) of their original respiration rate when darkened again.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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Figure 4: Respiration rates of R. litoralis cells. A: exponential growth phase; B: stationary growth phase. The values in mV min-1 indicate the respiration rates in the respective time intervals. Cells were kept anoxic under nitrogen gas until oxygen was supplied. At the beginning of each respiration measurement the cell suspension was saturated with oxygen and the oxygen consumption of the cells was measured in mV min-1. The response of R. litoralis to light differs remarkably between the two growth phases. During the exponential growth phase the initial respiration rate in the dark was higher (220 mV min-1) than in the stationary growth phase (140 mV min-1). When exposed to light, the cells that were in the exponential growth phase showed only a slight decrease to 200 mV min-1 (10%) of the respiration rate whereas in the stationary phase culture the respiration rate was reduced to 43% (60 mV min-1) of the original rate in the first light period and to 25% (30 mV min-1) in the second. Cells resumed 95% (exponential growth phase) and 86% (stationary growth phase) of their original respiration rate when darkened again.
Mentions: To confirm the functionality of the plasmid-encoded photosynthesis apparatus in R. litoralis, the photosynthetic activity of the strain was measured via oxygen consumption (Figure 4). Whereas almost no reaction to light was observed during growth, cells in the stationary growth phase were highly responsive to light and showed a reduced respiration rate when exposed to light (Figure 4). Even though pigmentation occurred already during the exponential growth phase, the organism did not use the photosynthetic apparatus until the culture reached the stationary growth phase. The use, but not the expression, of the photosynthesis apparatus might therefore be influenced by nutrient availability in R. litoralis, as stationary phase cultures are nutrient depleted. We obtained similar results for R. denitrificans, with cells in the late stationary phase showing a stronger response to light than cells from the exponential growth phase (data not shown). For the alpha-Proteobacteria Labrenzia alexandrii DFl-11 and Hoeflea phototrophica DFL-43 periodic nutrient starvation has been reported to trigger bacteriochlorophyll-a production whereas only slight effects were observed for D. shibae [40]. Obviously, the regulation mechanisms differ between the aerobic phototrophic bacteria and so does the architecture of their photosynthesis genes. In Additional File 3, the organization of the photosynthesis gene clusters of the organisms mentioned above is compared, showing that organisms with similar physiological traits also have similar gene organizations. The suggestion that the organization of genes within purple bacterial photosynthesis gene clusters reflects regulatory mechanisms, evolutionary history, and relationships between species was also made by other authors [7,41,42]. In the oligotrophic environment of the ocean, the use of the photosynthesis apparatus during nutrient depletion may be an important advantage for Roseobacter species in the competition with non-photosynthetic organisms.

Bottom Line: The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements.Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data.The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.

ABSTRACT

Background: Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis.

Results: The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype.

Conclusions: The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149_94 was probably translocated from the chromosome. Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have a common ancestor and are important for cell envelope biosynthesis. Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data. The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.

Show MeSH
Related in: MedlinePlus