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Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)).

Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Abt B, Verbarg S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T - Stand Genomic Sci (2011)

Bottom Line: Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae.The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules.This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae.

View Article: PubMed Central - PubMed

ABSTRACT
Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2(T) is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

No MeSH data available.


Related in: MedlinePlus

Scanning electron micrograph of T. nivea JP2T
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f2: Scanning electron micrograph of T. nivea JP2T

Mentions: Cells of strain JP2T are rod shaped with various lengths (Figure 2). Cultures of T. nivea contain gliding gonidia, filaments and rosettes (= aggregations of gonidial cells, not visible in Figure 2) [1]. The presence of a sheath was first reported in the 19th century [2] and later confirmed for the neotype strain [1]. The sheath contains several separate layers [1] of so far unknown structure. Motility was observed, but no flagella [1]. Numerous genes allocated to the functional role category motility were identified in the genome (see below). Many of these genes might be involved in the formation of the polar located fimbriae [32]. The typical rosettes generated by T. nivea are known from sulfide-containing waters [1,2]. Sulfur granules are invaginated by the cells, as reported in detail by Larkin and Shinabarger [1]. Strain JP2T stains Gram-negative, and grows only aerobically, best within a temperature range of 20 – 30°C [1]. Both the neotype strain and reference strain JP1 produce oxidase, but not catalase. The strains also produce poly-β-hydroxybutyrate [1]. Strain JP2T uses only four carbon sources; acetate, malate, pyruvate and oxalacetate [1]. Ammonia and nitrate (but not nitrite) are used as sole nitrogen sources [1]. The sole sulfur sources are sulfide and thiosulfate. What remains unresolved, based on the literature is whether or not T. nivea is autotrophic, obtaining carbon from CO2 and energy via oxidation of sulfide as reported by Winogradsky [13] or not, as reported by Larkin and Shinabarger [1]. In the case in which strain JP2T could use CO2 as a carbon source as well as acetate, malate, pyruvate and oxalacetate, while oxidizing the reduced sulfur compounds, it could be considered to be a mixotroph [1].


Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)).

Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Abt B, Verbarg S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T - Stand Genomic Sci (2011)

Scanning electron micrograph of T. nivea JP2T
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368414&req=5

f2: Scanning electron micrograph of T. nivea JP2T
Mentions: Cells of strain JP2T are rod shaped with various lengths (Figure 2). Cultures of T. nivea contain gliding gonidia, filaments and rosettes (= aggregations of gonidial cells, not visible in Figure 2) [1]. The presence of a sheath was first reported in the 19th century [2] and later confirmed for the neotype strain [1]. The sheath contains several separate layers [1] of so far unknown structure. Motility was observed, but no flagella [1]. Numerous genes allocated to the functional role category motility were identified in the genome (see below). Many of these genes might be involved in the formation of the polar located fimbriae [32]. The typical rosettes generated by T. nivea are known from sulfide-containing waters [1,2]. Sulfur granules are invaginated by the cells, as reported in detail by Larkin and Shinabarger [1]. Strain JP2T stains Gram-negative, and grows only aerobically, best within a temperature range of 20 – 30°C [1]. Both the neotype strain and reference strain JP1 produce oxidase, but not catalase. The strains also produce poly-β-hydroxybutyrate [1]. Strain JP2T uses only four carbon sources; acetate, malate, pyruvate and oxalacetate [1]. Ammonia and nitrate (but not nitrite) are used as sole nitrogen sources [1]. The sole sulfur sources are sulfide and thiosulfate. What remains unresolved, based on the literature is whether or not T. nivea is autotrophic, obtaining carbon from CO2 and energy via oxidation of sulfide as reported by Winogradsky [13] or not, as reported by Larkin and Shinabarger [1]. In the case in which strain JP2T could use CO2 as a carbon source as well as acetate, malate, pyruvate and oxalacetate, while oxidizing the reduced sulfur compounds, it could be considered to be a mixotroph [1].

Bottom Line: Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae.The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules.This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae.

View Article: PubMed Central - PubMed

ABSTRACT
Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2(T) is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

No MeSH data available.


Related in: MedlinePlus