1887

Abstract

In order to assess the potential of several molecular targets for the identification, typing and traceability of cyanobacteria in freshwater reservoirs, molecular techniques were applied to 118 cyanobacterial isolates mostly sourced from Portuguese freshwater reservoirs and representative of three orders of cyanobacteria: Chroococcales (54), Oscillatoriales (15) and Nostocales (49). The isolates were previously identified by morphological methods and subsequently characterized by composite hierarchical cluster analysis of STRR and LTRR (short and long tandemly repeated repetitive sequences) PCR fingerprinting profiles. Representative isolates were selected from each cluster and their molecular identification, at the species level, was obtained or confirmed by phylogenetic positioning using 16S rRNA gene and phylogenies. A highly congruent association was observed between STTR- and LTRR-based clusters and taxonomic affiliation, revealing the usefulness of such PCR fingerprinting profiles for the identification of cyanobacteria. Composite analysis of hierarchical clustering of M13 and ERIC PCR fingerprints also appeared suitable for strain typing and traceability within a reservoir, indicating its potential for use in cyanobacterial monitoring, as a quality management control. Based on Simpson () and Shannon–Wiener (′) indices a high diversity was observed within all species, with showing the lowest diversity values (=0.83; ′=0.88) and the highest ones (=′=0.99). A diagnostic key based on 16S-ARDRA, ITS amplification and ITS-ARDRA for identification purposes is also presented.

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2009-02-01
2019-10-19
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Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

PDF

Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

PDF

Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

PDF

Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

PDF

Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

PDF

Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

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Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

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Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

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Cyanobacterial isolates used in this study and GenBank accession numbers for 16S rDNA and sequences [ PDF] (26 kb) . Morphological characteristics of the cyanobacterial species, used to perform their identification [ PDF] (480 kb) MrBayes tree of the species belonging to the Chroococcales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (330 kb) MrBayes tree of the species belonging to the Oscillatoriales order using 1182 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (340 kb) MrBayes tree of the species belonging to the Nostocales order using 1203 nt of the 16S rRNA gene sequences in the alignment. The posterior probabilities values, above 50, are indicated to provide branch support. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (360 kb) (a) Global neighbour-joining tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Neighbour-joining tree of the sequences using 452 nt in the alignment. Percentage bootstrap values of 1000 replicates are given at each node. Bar: 10% sequence divergence. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (445 kb) (a) Global maximum-parsimony tree of representative species using 1182 nt of the rRNA gene sequences in the alignment. (b) Maximum-parsimony tree of the sequences using 452 nt in the alignment. GenBank accession numbers are indicated after species designation (names in bold-face correspond to sequences determined in this study). [ PDF] (415 kb) Representative M13 (a) and ERIC (b) fingerprinting profiles of the cyanobacterial species comprising more than five isolates; M: 1 kb plus molecular ladder. [ PDF] (1480 kb) Composite analysis of hierarchical clustering based on the M13 and ERIC PCR fingerprints of all isolates. [ PDF] (1220 kb)

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