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Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).

Schleheck D, Weiss M, Pitluck S, Bruce D, Land ML, Han S, Saunders E, Tapia R, Detter C, Brettin T, Han J, Woyke T, Goodwin L, Pennacchio L, Nolan M, Cook AM, Kjelleberg S, Thomas T - Stand Genomic Sci (2011)

Bottom Line: Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria.Here we describe the features of this organism, together with the complete genome sequence and annotation.The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

View Article: PubMed Central - PubMed

ABSTRACT
Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of 16S rRNA gene sequences showing the position of P. lavamentivorans DS-1T relative to other type strains within the families Rhodobiaceae, Phyllobacteriaceae and other families in the order Rhizobiales (see the text). Strains within the Rhodobiaceae and Phyllobacteriaceae shown in bold have genome projects underway or completed. The corresponding 16S rRNA gene accession numbers (or draft genome sequence identifiers) are indicated. The sequences were aligned using the GreenGenes NAST alignment tool [37]; neighbor-joining tree building and visualization involved the CLUSTAL and DENDROSCOPE software [38]. Caulobacterales sequences were used as outgroup. Bootstrap values >30 % are indicated; bar, 0.01 substitutions per nucleotide position.
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f2: Phylogenetic tree of 16S rRNA gene sequences showing the position of P. lavamentivorans DS-1T relative to other type strains within the families Rhodobiaceae, Phyllobacteriaceae and other families in the order Rhizobiales (see the text). Strains within the Rhodobiaceae and Phyllobacteriaceae shown in bold have genome projects underway or completed. The corresponding 16S rRNA gene accession numbers (or draft genome sequence identifiers) are indicated. The sequences were aligned using the GreenGenes NAST alignment tool [37]; neighbor-joining tree building and visualization involved the CLUSTAL and DENDROSCOPE software [38]. Caulobacterales sequences were used as outgroup. Bootstrap values >30 % are indicated; bar, 0.01 substitutions per nucleotide position.

Mentions: Based on the 16S rRNA gene sequence, strain DS-1T was described as the novel genus Parvibaculum, which was originally placed in the family Phyllobacteriaceae within the order Rhizobiales of Alphaproteobacteria [3,31]. The nearest well-described organism to strain DS-1T is Afifella marina (formerly Rhodobium marinum) (92% 16S rRNA gene sequence identity), a photosynthetic purple, non-sulfur bacterium. The genus Rhodobium was later re-classified as a member of the novel family Rhodobiaceae [26,32], together with two novel genera of other photosynthetic purple non-sulfur bacteria (Afifella and Roseospirillum), as well as with two novel genera of heterotrophic aerobic bacteria, represented by the red-pigmented Anderseniella baltica (gen. nov., sp. nov.) [33,34] and non-pigmented Tepidamorphus gemmatus (gen. nov., sp. nov.) [35,36]. A phylogenetic tree (Figure 2) was constructed with the 16S rRNA gene sequence of P. lavamentivorans DS-1T and that of (i) other isolated Parvibaculum strains, (ii) representatives of other genera within the family Rhodobiaceae, (iii) representatives of the genera in the family Phyllobacteriaceae, as well as, (iv) representatives of other families within the order Rhizobiales. The phylogenetic tree shows now the placement of Parvibaculum species within the family Rhodobiaceae, and that the Parvibaculum sequences clustered as a distinct evolutionary lineage within this family (Figure 2). This classification of Parvibaculum has been adopted in the Ribosomal Database Project (RDP) and SILVA rRNA Database Project, but not in the GreenGenes database. The family Rhodobiaceae has also not been included in the NCBI-taxonomy, IMG-taxonomy, and GOLD databases.


Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).

Schleheck D, Weiss M, Pitluck S, Bruce D, Land ML, Han S, Saunders E, Tapia R, Detter C, Brettin T, Han J, Woyke T, Goodwin L, Pennacchio L, Nolan M, Cook AM, Kjelleberg S, Thomas T - Stand Genomic Sci (2011)

Phylogenetic tree of 16S rRNA gene sequences showing the position of P. lavamentivorans DS-1T relative to other type strains within the families Rhodobiaceae, Phyllobacteriaceae and other families in the order Rhizobiales (see the text). Strains within the Rhodobiaceae and Phyllobacteriaceae shown in bold have genome projects underway or completed. The corresponding 16S rRNA gene accession numbers (or draft genome sequence identifiers) are indicated. The sequences were aligned using the GreenGenes NAST alignment tool [37]; neighbor-joining tree building and visualization involved the CLUSTAL and DENDROSCOPE software [38]. Caulobacterales sequences were used as outgroup. Bootstrap values >30 % are indicated; bar, 0.01 substitutions per nucleotide position.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368416&req=5

f2: Phylogenetic tree of 16S rRNA gene sequences showing the position of P. lavamentivorans DS-1T relative to other type strains within the families Rhodobiaceae, Phyllobacteriaceae and other families in the order Rhizobiales (see the text). Strains within the Rhodobiaceae and Phyllobacteriaceae shown in bold have genome projects underway or completed. The corresponding 16S rRNA gene accession numbers (or draft genome sequence identifiers) are indicated. The sequences were aligned using the GreenGenes NAST alignment tool [37]; neighbor-joining tree building and visualization involved the CLUSTAL and DENDROSCOPE software [38]. Caulobacterales sequences were used as outgroup. Bootstrap values >30 % are indicated; bar, 0.01 substitutions per nucleotide position.
Mentions: Based on the 16S rRNA gene sequence, strain DS-1T was described as the novel genus Parvibaculum, which was originally placed in the family Phyllobacteriaceae within the order Rhizobiales of Alphaproteobacteria [3,31]. The nearest well-described organism to strain DS-1T is Afifella marina (formerly Rhodobium marinum) (92% 16S rRNA gene sequence identity), a photosynthetic purple, non-sulfur bacterium. The genus Rhodobium was later re-classified as a member of the novel family Rhodobiaceae [26,32], together with two novel genera of other photosynthetic purple non-sulfur bacteria (Afifella and Roseospirillum), as well as with two novel genera of heterotrophic aerobic bacteria, represented by the red-pigmented Anderseniella baltica (gen. nov., sp. nov.) [33,34] and non-pigmented Tepidamorphus gemmatus (gen. nov., sp. nov.) [35,36]. A phylogenetic tree (Figure 2) was constructed with the 16S rRNA gene sequence of P. lavamentivorans DS-1T and that of (i) other isolated Parvibaculum strains, (ii) representatives of other genera within the family Rhodobiaceae, (iii) representatives of the genera in the family Phyllobacteriaceae, as well as, (iv) representatives of other families within the order Rhizobiales. The phylogenetic tree shows now the placement of Parvibaculum species within the family Rhodobiaceae, and that the Parvibaculum sequences clustered as a distinct evolutionary lineage within this family (Figure 2). This classification of Parvibaculum has been adopted in the Ribosomal Database Project (RDP) and SILVA rRNA Database Project, but not in the GreenGenes database. The family Rhodobiaceae has also not been included in the NCBI-taxonomy, IMG-taxonomy, and GOLD databases.

Bottom Line: Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria.Here we describe the features of this organism, together with the complete genome sequence and annotation.The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

View Article: PubMed Central - PubMed

ABSTRACT
Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

No MeSH data available.


Related in: MedlinePlus