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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.


Maximum likelihood phylogenetic tree based on 16S rDNA reference sequences (available in the ARB database) with the subsequent addition of 64 contigs of 16S rDNA retrieved from the consortium (listed in Fig. S1. Due to graphic requirements, the branches between ingroup and outgroup are not shown entirely, the full tree is available in the Supplementary Material). Phylogenetically-related contigs have been enclosed, for clarity, in a box together with their closest relatives. A total of 23 such groups were identified, nine among Gammaproteobacteria, one among Betaproteobacteria, six among Alphaproteobacteria, one among Verrucomicrobia, five among Bacteroidetes, and one among Planctomycetes
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Fig3: Maximum likelihood phylogenetic tree based on 16S rDNA reference sequences (available in the ARB database) with the subsequent addition of 64 contigs of 16S rDNA retrieved from the consortium (listed in Fig. S1. Due to graphic requirements, the branches between ingroup and outgroup are not shown entirely, the full tree is available in the Supplementary Material). Phylogenetically-related contigs have been enclosed, for clarity, in a box together with their closest relatives. A total of 23 such groups were identified, nine among Gammaproteobacteria, one among Betaproteobacteria, six among Alphaproteobacteria, one among Verrucomicrobia, five among Bacteroidetes, and one among Planctomycetes

Mentions: Figure 3 shows the phylogenetic tree based on the 16S rDNA sequences selected from the NCBI nucleotide database with the added consortium contigs. At the higher taxonomic levels, the tree reflected almost perfectly the results of the BLASTn analysis. Additionally, in most cases, it was possible to recognize the affiliation of the contigs to the family or even genus rank. Several contigs cluster with bacterial sequences derived from habitats which share similarities to the Antarctic environment where the original sample of E. focardii was collected, such as the Alaskian Byron glacier [39], Arctic and Antarctic coastal seawaters, or other cold environments (e.g., Colwellia psychrerythraea, Ahrensia kielensis, Octadecabacter arcticus, etc.) [40–42]. Furthermore, we detected phylogenetic relationships to sequences retrieved from bacteria living in tight association with eukaryotic organisms (e.g., Arenibacter echinorum, originally isolated from the sea urchin Strongylocentrotus intermedius, and Porticoccus hydrocarbonoclasticus, found associated with the dinoflagellate Lingulodinium polyedrum) [43, 44], and, notably, even to genera that encompass endosymbionts of ciliates (i.e., Francisella and Devosia) [10, 45]. We additionally observed that some contigs are affiliated with organisms characterized by special metabolic repertoires (e.g. Marinosulfonomonas methylotropha, Methylotenera mobilis or P. hydrocarbonoclasticus) [43, 46] or possess genomes rich in transposases and other mobile genetic elements (genus Octadecabacter) [47].Fig. 3


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)

Maximum likelihood phylogenetic tree based on 16S rDNA reference sequences (available in the ARB database) with the subsequent addition of 64 contigs of 16S rDNA retrieved from the consortium (listed in Fig. S1. Due to graphic requirements, the branches between ingroup and outgroup are not shown entirely, the full tree is available in the Supplementary Material). Phylogenetically-related contigs have been enclosed, for clarity, in a box together with their closest relatives. A total of 23 such groups were identified, nine among Gammaproteobacteria, one among Betaproteobacteria, six among Alphaproteobacteria, one among Verrucomicrobia, five among Bacteroidetes, and one among Planctomycetes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Maximum likelihood phylogenetic tree based on 16S rDNA reference sequences (available in the ARB database) with the subsequent addition of 64 contigs of 16S rDNA retrieved from the consortium (listed in Fig. S1. Due to graphic requirements, the branches between ingroup and outgroup are not shown entirely, the full tree is available in the Supplementary Material). Phylogenetically-related contigs have been enclosed, for clarity, in a box together with their closest relatives. A total of 23 such groups were identified, nine among Gammaproteobacteria, one among Betaproteobacteria, six among Alphaproteobacteria, one among Verrucomicrobia, five among Bacteroidetes, and one among Planctomycetes
Mentions: Figure 3 shows the phylogenetic tree based on the 16S rDNA sequences selected from the NCBI nucleotide database with the added consortium contigs. At the higher taxonomic levels, the tree reflected almost perfectly the results of the BLASTn analysis. Additionally, in most cases, it was possible to recognize the affiliation of the contigs to the family or even genus rank. Several contigs cluster with bacterial sequences derived from habitats which share similarities to the Antarctic environment where the original sample of E. focardii was collected, such as the Alaskian Byron glacier [39], Arctic and Antarctic coastal seawaters, or other cold environments (e.g., Colwellia psychrerythraea, Ahrensia kielensis, Octadecabacter arcticus, etc.) [40–42]. Furthermore, we detected phylogenetic relationships to sequences retrieved from bacteria living in tight association with eukaryotic organisms (e.g., Arenibacter echinorum, originally isolated from the sea urchin Strongylocentrotus intermedius, and Porticoccus hydrocarbonoclasticus, found associated with the dinoflagellate Lingulodinium polyedrum) [43, 44], and, notably, even to genera that encompass endosymbionts of ciliates (i.e., Francisella and Devosia) [10, 45]. We additionally observed that some contigs are affiliated with organisms characterized by special metabolic repertoires (e.g. Marinosulfonomonas methylotropha, Methylotenera mobilis or P. hydrocarbonoclasticus) [43, 46] or possess genomes rich in transposases and other mobile genetic elements (genus Octadecabacter) [47].Fig. 3

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.