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Characterization of Streptomyces spp. isolated from the sea surface microlayer in the Trondheim Fjord, Norway.

Hakvåg S, Fjaervik E, Josefsen KD, Ian E, Ellingsen TE, Zotchev SB - Mar Drugs (2008)

Bottom Line: Sequencing and phylogenetic analysis of the PKS gene fragments revealed that horizontal gene transfer between closely related species might have taken place.Identification of unique PKS genes in these isolates implies that de-replication can not be performed based solely on the 16S rDNA sequences.The results obtained in this study suggest that streptomycetes from the neuston population may be an interesting source for discovery of new antimicrobial agents.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway. sigrid.hakvag@biotech.ntnu.no

ABSTRACT
The water surface microlayer is still poorly explored, although it has been shown to contain a high density of metabolically active bacteria, often called bacterioneuston. Actinomycetes from the surface microlayer in the Trondheim fjord, Norway, have been isolated and characterized. A total of 217 isolates from two separate samples morphologically resembling the genus Streptomyces have been further investigated in this study. Antimicrobial assays showed that about 80% of the isolates exhibited antagonistic activity against non-filamentous fungus, Gram-negative, and Gram-positive bacteria. Based on the macroscopic analyses and inhibition patterns from the antimicrobial assays, the sub-grouping of isolates was performed. Partial 16S rDNAs from the candidates from each subgroup were sequenced and phylogenetic analysis performed. 7 isolates with identical 16S rDNA sequences were further studied for the presence of PKS type I genes. Sequencing and phylogenetic analysis of the PKS gene fragments revealed that horizontal gene transfer between closely related species might have taken place. Identification of unique PKS genes in these isolates implies that de-replication can not be performed based solely on the 16S rDNA sequences. The results obtained in this study suggest that streptomycetes from the neuston population may be an interesting source for discovery of new antimicrobial agents.

Show MeSH
Phylogenetic relationship between PKS type I amino acid sequences from streptomycete isolates with identical partial 16S rDNA sequences. Closest matches from the BLAST searches are also included. Putative distinct KS domain types are indicated with letters (A, B, C etc). Numbers at tree nodes represent the number of times the topology to the right of the node was recovered in 1000 bootstrap re-samplings. Accession numbers for the sequences are given in parentheses. Scale bar represents the number of changes per amino acid position.
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f3-md-06-00620: Phylogenetic relationship between PKS type I amino acid sequences from streptomycete isolates with identical partial 16S rDNA sequences. Closest matches from the BLAST searches are also included. Putative distinct KS domain types are indicated with letters (A, B, C etc). Numbers at tree nodes represent the number of times the topology to the right of the node was recovered in 1000 bootstrap re-samplings. Accession numbers for the sequences are given in parentheses. Scale bar represents the number of changes per amino acid position.

Mentions: In order to visualize taxonomic relationship between the amino acid sequences encoded by the PCR-amplified fragments, a phylogenetic tree was constructed, which also included sequences from the best matches according to the BLAST search. The architecture of the tree, presented in Figure 3, clearly shows some discrepancy between the BLAST search and the phylogenetic analysis. For example, the PKSI-1,-2,-3 and -6 sequences from the isolate MP8E7 do not cluster with the corresponding best matches from the BLAST search, and form a separate branch on the tree. This suggests that the PKS gene cluster represented by these sequences might have evolved separately, and potentially can encode a novel polyketide metabolite.


Characterization of Streptomyces spp. isolated from the sea surface microlayer in the Trondheim Fjord, Norway.

Hakvåg S, Fjaervik E, Josefsen KD, Ian E, Ellingsen TE, Zotchev SB - Mar Drugs (2008)

Phylogenetic relationship between PKS type I amino acid sequences from streptomycete isolates with identical partial 16S rDNA sequences. Closest matches from the BLAST searches are also included. Putative distinct KS domain types are indicated with letters (A, B, C etc). Numbers at tree nodes represent the number of times the topology to the right of the node was recovered in 1000 bootstrap re-samplings. Accession numbers for the sequences are given in parentheses. Scale bar represents the number of changes per amino acid position.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2630845&req=5

f3-md-06-00620: Phylogenetic relationship between PKS type I amino acid sequences from streptomycete isolates with identical partial 16S rDNA sequences. Closest matches from the BLAST searches are also included. Putative distinct KS domain types are indicated with letters (A, B, C etc). Numbers at tree nodes represent the number of times the topology to the right of the node was recovered in 1000 bootstrap re-samplings. Accession numbers for the sequences are given in parentheses. Scale bar represents the number of changes per amino acid position.
Mentions: In order to visualize taxonomic relationship between the amino acid sequences encoded by the PCR-amplified fragments, a phylogenetic tree was constructed, which also included sequences from the best matches according to the BLAST search. The architecture of the tree, presented in Figure 3, clearly shows some discrepancy between the BLAST search and the phylogenetic analysis. For example, the PKSI-1,-2,-3 and -6 sequences from the isolate MP8E7 do not cluster with the corresponding best matches from the BLAST search, and form a separate branch on the tree. This suggests that the PKS gene cluster represented by these sequences might have evolved separately, and potentially can encode a novel polyketide metabolite.

Bottom Line: Sequencing and phylogenetic analysis of the PKS gene fragments revealed that horizontal gene transfer between closely related species might have taken place.Identification of unique PKS genes in these isolates implies that de-replication can not be performed based solely on the 16S rDNA sequences.The results obtained in this study suggest that streptomycetes from the neuston population may be an interesting source for discovery of new antimicrobial agents.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway. sigrid.hakvag@biotech.ntnu.no

ABSTRACT
The water surface microlayer is still poorly explored, although it has been shown to contain a high density of metabolically active bacteria, often called bacterioneuston. Actinomycetes from the surface microlayer in the Trondheim fjord, Norway, have been isolated and characterized. A total of 217 isolates from two separate samples morphologically resembling the genus Streptomyces have been further investigated in this study. Antimicrobial assays showed that about 80% of the isolates exhibited antagonistic activity against non-filamentous fungus, Gram-negative, and Gram-positive bacteria. Based on the macroscopic analyses and inhibition patterns from the antimicrobial assays, the sub-grouping of isolates was performed. Partial 16S rDNAs from the candidates from each subgroup were sequenced and phylogenetic analysis performed. 7 isolates with identical 16S rDNA sequences were further studied for the presence of PKS type I genes. Sequencing and phylogenetic analysis of the PKS gene fragments revealed that horizontal gene transfer between closely related species might have taken place. Identification of unique PKS genes in these isolates implies that de-replication can not be performed based solely on the 16S rDNA sequences. The results obtained in this study suggest that streptomycetes from the neuston population may be an interesting source for discovery of new antimicrobial agents.

Show MeSH