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Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences.

Pucciarelli S, Devaraj RR, Mancini A, Ballarini P, Castelli M, Schrallhammer M, Petroni G, Miceli C - Microb. Ecol. (2015)

Bottom Line: Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity".To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition.Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, 62032, Italy, sandra.pucciarelli@unicam.it.

ABSTRACT
We report the characterization of the bacterial consortium associated to Euplotes focardii, a strictly psychrophilic marine ciliate that was maintained in laboratory cultures at 4 °C after its first isolation from Terra Nova Bay, in Antarctica. By Illumina genome analyser, we obtained 11,179 contigs of potential prokaryotic origin and classified them according to the NCBI's prokaryotic attributes table. The majority of these sequences correspond to either Bacteroidetes (16 %) or Proteobacteria (78 %). The latter were dominated by gamma- (39 %, including sequences related to the pathogenic genus Francisella), and alpha-proteobacterial (30 %) sequences. Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity". Furthermore, we identified genes that encode for enzymes involved in the catabolism of complex substance for energy reserves. We also characterized members of the transposase and integrase superfamilies, whose role in bacterial evolution is well documented, as well as putative antifreeze proteins. Antibiotic treatments of E. focardii cultures delayed the cell division of the ciliate. To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition. Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.

No MeSH data available.


Gene Ontology (GO) annotation of the dataset from the three most represented bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) for molecular function (a) and biological processes (b). In each panel are reported rounded off percentages of the represented terms. In cases in which rounded off percentage values were identical for the three bacterial groups, only one value is reported in black (e.g., ion binding, 9 %); in cases in which rounded off percentage values were differing in the three group, the different values are reported in red and they, respectively, refer to Gammaproteobacteria (g), Alphaproteobacteria (a), and Bacteroidetes (b)
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Fig4: Gene Ontology (GO) annotation of the dataset from the three most represented bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) for molecular function (a) and biological processes (b). In each panel are reported rounded off percentages of the represented terms. In cases in which rounded off percentage values were identical for the three bacterial groups, only one value is reported in black (e.g., ion binding, 9 %); in cases in which rounded off percentage values were differing in the three group, the different values are reported in red and they, respectively, refer to Gammaproteobacteria (g), Alphaproteobacteria (a), and Bacteroidetes (b)

Mentions: Gene Ontology (GO) annotation was performed for contigs belonging to the three dominant taxa, i.e.,Gammaproteobacteria (g), Alphaproteobacteria (a), and Bacteroidetes (b) (Fig. 4). A gene description and GO classification based on the “best hit” from the blastx search was assigned to each contig. For simplicity, only the categories of the three bacterial groups whose rounded off values were 1 % or higher were reported (Fig. 4). In the three groups, the most frequent Molecular Function categories were “small molecule binding” (19 % (g), 19 % (a), and 17 % (b), respectively), hydrolase activity (13 % (g), 13 % (a), and 15 % (b)), nucleic acid binding (12 % (g), 12 % (a), 13 % (b)), transferase activity (11 %), ion binding (9 %), and oxidoreductase activity (8 %). For the “Biological Process” categories, the largest number of contigs corresponded to molecules involved in cellular metabolic processes (17 %), primary metabolic processes (17 %), and nitrogen metabolism (11 %) (Fig. 4b).Fig. 4


Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences.

Pucciarelli S, Devaraj RR, Mancini A, Ballarini P, Castelli M, Schrallhammer M, Petroni G, Miceli C - Microb. Ecol. (2015)

Gene Ontology (GO) annotation of the dataset from the three most represented bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) for molecular function (a) and biological processes (b). In each panel are reported rounded off percentages of the represented terms. In cases in which rounded off percentage values were identical for the three bacterial groups, only one value is reported in black (e.g., ion binding, 9 %); in cases in which rounded off percentage values were differing in the three group, the different values are reported in red and they, respectively, refer to Gammaproteobacteria (g), Alphaproteobacteria (a), and Bacteroidetes (b)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig4: Gene Ontology (GO) annotation of the dataset from the three most represented bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) for molecular function (a) and biological processes (b). In each panel are reported rounded off percentages of the represented terms. In cases in which rounded off percentage values were identical for the three bacterial groups, only one value is reported in black (e.g., ion binding, 9 %); in cases in which rounded off percentage values were differing in the three group, the different values are reported in red and they, respectively, refer to Gammaproteobacteria (g), Alphaproteobacteria (a), and Bacteroidetes (b)
Mentions: Gene Ontology (GO) annotation was performed for contigs belonging to the three dominant taxa, i.e.,Gammaproteobacteria (g), Alphaproteobacteria (a), and Bacteroidetes (b) (Fig. 4). A gene description and GO classification based on the “best hit” from the blastx search was assigned to each contig. For simplicity, only the categories of the three bacterial groups whose rounded off values were 1 % or higher were reported (Fig. 4). In the three groups, the most frequent Molecular Function categories were “small molecule binding” (19 % (g), 19 % (a), and 17 % (b), respectively), hydrolase activity (13 % (g), 13 % (a), and 15 % (b)), nucleic acid binding (12 % (g), 12 % (a), 13 % (b)), transferase activity (11 %), ion binding (9 %), and oxidoreductase activity (8 %). For the “Biological Process” categories, the largest number of contigs corresponded to molecules involved in cellular metabolic processes (17 %), primary metabolic processes (17 %), and nitrogen metabolism (11 %) (Fig. 4b).Fig. 4

Bottom Line: Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity".To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition.Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, 62032, Italy, sandra.pucciarelli@unicam.it.

ABSTRACT
We report the characterization of the bacterial consortium associated to Euplotes focardii, a strictly psychrophilic marine ciliate that was maintained in laboratory cultures at 4 °C after its first isolation from Terra Nova Bay, in Antarctica. By Illumina genome analyser, we obtained 11,179 contigs of potential prokaryotic origin and classified them according to the NCBI's prokaryotic attributes table. The majority of these sequences correspond to either Bacteroidetes (16 %) or Proteobacteria (78 %). The latter were dominated by gamma- (39 %, including sequences related to the pathogenic genus Francisella), and alpha-proteobacterial (30 %) sequences. Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity". Furthermore, we identified genes that encode for enzymes involved in the catabolism of complex substance for energy reserves. We also characterized members of the transposase and integrase superfamilies, whose role in bacterial evolution is well documented, as well as putative antifreeze proteins. Antibiotic treatments of E. focardii cultures delayed the cell division of the ciliate. To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition. Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.

No MeSH data available.