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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.


Microbial attributes of the E. focardii bacterial consortium dataset
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Related In: Results  -  Collection


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Fig1: Microbial attributes of the E. focardii bacterial consortium dataset

Mentions: By Illumina genome analyser, we obtained 11,179 contigs lacking at their ends the 5′-CCCCAAAA-3′/3′-GGGGTTTT-5′ telomeric repeats characteristic of the Euplotes nanochromosomes. These contigs ranged in size from 100 to 25,584 bp and did not correspond to any eukaryotic sequences after binning. Therefore, these contigs were considered to be of potential prokaryotic origin (termed here microbial dataset). Comparison to NCBI’s prokaryotic attributes table showed that about 2600 of the entries were attributed to the categories “marine environment” and “Gram-negative bacteria” (Fig. 1). More than 2100 entries were associated to “motile bacteria”, and nearly 600 entries were attributed to “psychrophilic microorganisms”. Proteobacteria (78 %) was the most abundant phylum of bacteria, represented mainly by Gammaproteobacteria (39 % of the total bacteria), followed by Alphaproteobacteria (30 %), and Betaproteobacteria (8 %) classes (Fig. 2a). Other sequences were classified as follows: Bacteroidetes (16 %) Firmicutes (2.64 %), Actinobacteria (1.22 %), Cyanobacteria (1.00 %), Chlamydiae/Verrucomicrobia (0.37 %), Planctomycetes (0.22 %), Spirochaetes (0.19 %), Acidobacteria (0.13 %), and Fusobacteria (0.09 %), whereas 0.45 % of the contigs affiliated to sequences from Archaea (due to the low number of Archea sequences the consortium will be referred as bacterial consortium). A similar distribution of the most represented classes was obtained by analyzing the 70 contigs corresponding to partial sequences of the 16S rDNA gene (Fig. 2b).Fig. 1


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)

Microbial attributes of the E. focardii bacterial consortium dataset
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4494151&req=5

Fig1: Microbial attributes of the E. focardii bacterial consortium dataset
Mentions: By Illumina genome analyser, we obtained 11,179 contigs lacking at their ends the 5′-CCCCAAAA-3′/3′-GGGGTTTT-5′ telomeric repeats characteristic of the Euplotes nanochromosomes. These contigs ranged in size from 100 to 25,584 bp and did not correspond to any eukaryotic sequences after binning. Therefore, these contigs were considered to be of potential prokaryotic origin (termed here microbial dataset). Comparison to NCBI’s prokaryotic attributes table showed that about 2600 of the entries were attributed to the categories “marine environment” and “Gram-negative bacteria” (Fig. 1). More than 2100 entries were associated to “motile bacteria”, and nearly 600 entries were attributed to “psychrophilic microorganisms”. Proteobacteria (78 %) was the most abundant phylum of bacteria, represented mainly by Gammaproteobacteria (39 % of the total bacteria), followed by Alphaproteobacteria (30 %), and Betaproteobacteria (8 %) classes (Fig. 2a). Other sequences were classified as follows: Bacteroidetes (16 %) Firmicutes (2.64 %), Actinobacteria (1.22 %), Cyanobacteria (1.00 %), Chlamydiae/Verrucomicrobia (0.37 %), Planctomycetes (0.22 %), Spirochaetes (0.19 %), Acidobacteria (0.13 %), and Fusobacteria (0.09 %), whereas 0.45 % of the contigs affiliated to sequences from Archaea (due to the low number of Archea sequences the consortium will be referred as bacterial consortium). A similar distribution of the most represented classes was obtained by analyzing the 70 contigs corresponding to partial sequences of the 16S rDNA gene (Fig. 2b).Fig. 1

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.