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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.


Variable Pfam families and GO terms among the three most represented bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) done using CoMet [32]. The bar charts show the Pfam domain (a) and GO term categories (b) with the highest frequencies in the consortium (x-axis values), and the largest terms variation with respect to precomputed profiles obtained from microbial metagenomes in the CoMet server (y-axis values)
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Fig5: Variable Pfam families and GO terms among the three most represented bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) done using CoMet [32]. The bar charts show the Pfam domain (a) and GO term categories (b) with the highest frequencies in the consortium (x-axis values), and the largest terms variation with respect to precomputed profiles obtained from microbial metagenomes in the CoMet server (y-axis values)

Mentions: We also estimated the most represented functional categories in the three dominant bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) in the consortium with respect to the metagenome dataset available in the CoMet server [32]. The bar charts in Fig. 5a, b show the Pfam domain frequencies and GO term categories, respectively, with the highest frequencies in the consortium (x-axis values) and the largest terms variation compared to precomputed profiles obtained from microbial metagenomes in the CoMet server (y-axis values). This comparison is crucial for an understanding of community specific properties that are possibly linked with particular environmental factors. From this analysis, it resulted that the Pfam domain family with the largest variation with respect to the other microbial metagenomes is represented by proteins involved in transmembrane transport (Fig. 5a). The GO-terms analysis shows proteins involved in “oxidoreductase activity” at the highest value of variation, thus suggesting a high metabolic potential of the consortium to survive in an oxygen-rich environment, followed by the “catalytic activity” and “molecular function” terms (Fig. 5b).Fig. 5


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)

Variable Pfam families and GO terms among the three most represented bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) done using CoMet [32]. The bar charts show the Pfam domain (a) and GO term categories (b) with the highest frequencies in the consortium (x-axis values), and the largest terms variation with respect to precomputed profiles obtained from microbial metagenomes in the CoMet server (y-axis values)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4494151&req=5

Fig5: Variable Pfam families and GO terms among the three most represented bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) done using CoMet [32]. The bar charts show the Pfam domain (a) and GO term categories (b) with the highest frequencies in the consortium (x-axis values), and the largest terms variation with respect to precomputed profiles obtained from microbial metagenomes in the CoMet server (y-axis values)
Mentions: We also estimated the most represented functional categories in the three dominant bacterial groups (Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes) in the consortium with respect to the metagenome dataset available in the CoMet server [32]. The bar charts in Fig. 5a, b show the Pfam domain frequencies and GO term categories, respectively, with the highest frequencies in the consortium (x-axis values) and the largest terms variation compared to precomputed profiles obtained from microbial metagenomes in the CoMet server (y-axis values). This comparison is crucial for an understanding of community specific properties that are possibly linked with particular environmental factors. From this analysis, it resulted that the Pfam domain family with the largest variation with respect to the other microbial metagenomes is represented by proteins involved in transmembrane transport (Fig. 5a). The GO-terms analysis shows proteins involved in “oxidoreductase activity” at the highest value of variation, thus suggesting a high metabolic potential of the consortium to survive in an oxygen-rich environment, followed by the “catalytic activity” and “molecular function” terms (Fig. 5b).Fig. 5

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.