Open Access

Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2T)

  • Alla Lapidus
  • , Matt Nolan
  • , Susan Lucas
  • , Tijana Glavina Del Rio
  • , Hope Tice
  • , Jan-Fang Cheng
  • , Roxanne Tapia,
  • , Cliff Han,
  • , Lynne Goodwin,
  • , Sam Pitluck
  • , Konstantinos Liolios
  • , Ioanna Pagani
  • , Natalia Ivanova
  • , Marcel Huntemann
  • , Konstantinos Mavromatis
  • , Natalia Mikhailova
  • , Amrita Pati
  • , Amy Chen
  • , Krishna Palaniappan
  • , Miriam Land,
  • , Evelyne-Marie Brambilla
  • , Manfred Rohde
  • , Birte Abt
  • , Susanne Verbarg
  • , Markus Göker
  • , James Bristow
  • , Jonathan A. Eisen,
  • , Victor Markowitz
  • , Philip Hugenholtz,
  • , Nikos C. Kyrpides
  • , Hans-Peter Klenk
  • and Tanja Woyke
Corresponding author

DOI: 10.4056/sigs.2344929

Received: 30 December 2011

Published: 31 December 2011

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 JP2T 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.

Keywords:

strictly aerobicgliding motilityGram-negativemesophilesheathfilamentssulfur granulesThiotrichaceaeGEBA

Introduction

Strain JP2T (= DSM 5205 = ATCC 35100) is the type strain of Thiothrix nivea [1,2] which is the type species of the genus Thiothrix [1,2]. Cultures of the species were first observed and classified as “Beggiatoa nivea” in 1865 by Rabenhorst [3] and later (1888) placed into the novel genus Thiothrix by Winogradsky [2]. The species was included on the Approved List of Bacterial Names Amended edition in 1980 [4]. Axenic cultures isolated from sulfide-containing well water became available in 1980 through the work of J. M. Larkin [5], with the formal description of strain JP2T as the neotype strain of the species T. nivea in 1983 [1], as well as strain JP1 as a reference strain within the species [1]. The generic name derives from the Neo-Greek words theion, sulfur, and thrix, hair [6]. The species epithet is derived from the Latin word nivea snow-white [6]. The species became well known for its sulfur granules, the gliding motility and the typical rosettes [1], which were first observed by Winogradsky [2]. Here we present a summary classification and a set of features for T. nivea JP2T, together with the description of the complete genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of T. nivea JP2T was compared using NCBI BLAST [7] under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [8] and the relative frequencies of taxa and keywords (reduced to their stem [9]) were determined, weighted by BLAST scores. The most frequently occurring genus was Thiothrix (100.0%, 12 hits in total). Regarding the single hit to sequences from members of the species, the average identity within HSPs was 99.5%, whereas the average coverage by HSPs was 99.4%. Regarding the four hits to sequences from other members of the genus, the average identity within HSPs was 94.2%, whereas the average coverage by HSPs was 96.0%. Among all other species, the one yielding the highest score was, Thiothrix fructosivorans (GU269554) which corresponded to an identity of 94.5% and an HSP coverage of 100.0%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was AM490765 ('Linking and functional nutrient spiraling mats (USA) microbial mat sulfidic cave spring Lower Kane Cave Big Horn LKC22 clone SS LKC22 UB32'), which showed an identity of 96.7% and an HSP coverage of 100.0%. The most frequently occurring keywords within the labels of environmental samples which yielded hits were 'sulfid' (4.2%), 'microbi' (4.0%), 'biofilm' (3.4%), 'cave' (2.8%) and 'karst' (2.7%) (238 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found. These keywords reflect the ecological properties reported for the species and strain JP2T in the original description [1,2].

Figure 1 shows the phylogenetic neighborhood of T. nivea in a 16S rRNA based tree. The sequences of the two identical 16S rRNA gene copies in the genome do not differ from the previously published 16S rRNA sequence (L40993), which contains six ambiguous base calls.

Figure 1

Phylogenetic tree highlighting the position of T. nivea relative to the other type strains within the family Thiotrichaceae. The tree was inferred from 1,332 aligned characters [10,11] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [12]. Rooting was done initially using the midpoint method [13] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 200 ML bootstrap replicates [14] (left) and from 1,000 maximum parsimony bootstrap replicates [15] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [16] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks.

Table 1

Classification and general features of T. nivea JP2T according to the MIGS recommendations [17] and the NamesforLife database [18].

MIGS ID

    Property

     Term

     Evidence code

    Current classification

     Domain Bacteria

     TAS [19]

     Phylum “Proteobacteria

     TAS [20,21]

     Class Gammaproteobacteria

     TAS [22]

     Order Thiotrichales

     TAS [22,23]

     Family Thiotrichaceae

     TAS [22,24]

     Genus Thiothrix

     TAS [2,4,25-27]

     Species Thiothrix nivea

     TAS [1,5]

     Type strain JP2

     TAS [1]

    Gram stain

     negative

     TAS [1]

    Cell shape

     rod-shaped, filaments with a sheath, rosettes

     TAS [1]

    Motility

     gliding

     TAS [1]

    Sporulation

     not reported

    Temperature range

     mesophilic, 6-34°C

     TAS [1]

    Optimum temperature

     25-30°C

     TAS [1]

    Salinity

     not reported

MIGS-22

    Oxygen requirement

     strictly aerobic

     TAS [1]

    Carbon source

     acetate, malate, pyruvate, oxalacetate

     TAS [1]

    Energy metabolism

     chemolithotroph

     NAS

MIGS-6

    Habitat

     spring-generated, flowing, H2S-enriched waters,      deep sea hydrothermal vents

     TAS [28,29]

MIGS-15

    Biotic relationship

     free-living

     TAS [1]

MIGS-14

    Pathogenicity

     none

     TAS [1]

    Biosafety level

     1

     TAS [30]

    Isolation

     H2S-enriched well water

     TAS [1]

MIGS-4

    Geographic location

     John Pennycamp State Park, Key Largo, FL, USA

     TAS [1]

MIGS-5

    Sample collection time

     1983 or before

     NAS

MIGS-4.1

    Latitude

     25.13

     NAS

MIGS-4.2

    Longitude

     -80.41

     NAS

MIGS-4.3

    Depth

     not reported

MIGS-4.4

    Altitude

     not reported

Evidence codes - TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from of the Gene Ontology project [31].

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].

Figure 2

Scanning electron micrograph of T. nivea JP2T

Chemotaxonomy

There are no chemotaxonomic data on cell wall structure, cellular lipids, quinones or polar lipids of strain JP2T.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [33], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [34]. The genome project is deposited in the Genome On Line Database [16] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.

Table 2

Genome sequencing project information

MIGS ID

     Property

    Term

MIGS-31

     Finishing quality

    Improved-high-quality-draft

MIGS-28

     Libraries used

    Three genomic libraries: one 454 pyrosequence standard library,     one 454 PE library (12 kb insert size), one Illumina library

MIGS-29

     Sequencing platforms

    Illumina GAii, 454 GS FLX Titanium

MIGS-31.2

     Sequencing coverage

    111.5 × Illumina; 28.9 × pyrosequence

MIGS-30

     Assemblers

    Newbler version 2.3-PreRelease-6/30/2009, Velvet version 1.0.13, phrap SPS-4.24

MIGS-32

     Gene calling method

    Prodigal 1.4, GenePRIMP

     INSDC ID

    Not yet available

     Genbank Date of Release

    Not yet available

     GOLD ID

    Gi03023

     NCBI project ID

    51139

     Database: IMG-GEBA

    2506520049

MIGS-13

     Source material identifier

    DSM 5205

     Project relevance

    Tree of Life, GEBA

Growth conditions and DNA isolation

T. nivea JP2T, DSM 5205, was grown in DSMZ medium 1300 (Thiothrix Medium) [35] at 25°C. DNA was isolated from 0.5-1 g of cell paste using Jetflex Genomic DNA Purification Kit (GENOMED 600100) following the standard protocol as recommended by the manufacturer, but adding 10µl proteinase K for one hour extended lysis at 58°C. DNA is available through the DNA Bank Network [36].

Genome sequencing and assembly

The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [37]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 269 contigs in four scaffolds was converted into a phrap assembly by [38] making fake reads from the consensus to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (518.8 Mb) was assembled with Velvet [39], and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 162.5 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [38] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [37], Dupfinisher, or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 632 additional reactions were necessary to close gaps and to raise the quality of the final sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [40]. This genome is not finished. The improved high quality draft consists of 15 contigs in four scaffolds. Some mis-assemblies are possible in the final assembly. Together, the combination of the Illumina and 454 sequencing platforms provided 140.4 × coverage of the genome. The final assembly contained 444,417 pyrosequence and 14,381,947 Illumina reads.

Genome annotation

Genes were identified using Prodigal [41] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [42]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [43].

Genome properties

The genome consists in the current assembly of 15 contigs in four scaffolds with a length of 5,599 bp, 7,015 bp, 40,927 bp, and 4,638,170 bp, respectively, and a G+C content of 54.9% (Table 3). Of the 4,594 genes predicted, 4,542 were protein-coding genes, and 52 RNAs; 213 pseudogenes were also identified. The majority of the protein-coding genes (98.8%) were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Table 3

Genome Statistics

Attribute

    Value

     % of Total

Genome size (bp)

    4,691,711

     100.00%

DNA coding region (bp)

    4,147,061

     88.39%

DNA G+C content (bp)

    2,573,778

     54.87%

Number of scaffolds

    4

Number of contigs

    15

Total genes

    4,594

     100.00%

RNA genes

    52

     1.15%

rRNA operons

    2

Protein-coding genes

    4,542

     98.85%

Pseudo genes

    213

     4.64%

Genes with function prediction

    2,918

     63.52%

Genes in paralog clusters

    2,282

     49.67%

Genes assigned to COGs

    3,275

     71.29%

Genes assigned Pfam domains

    3,338

     72.66%

Genes with signal peptides

    971

     21.14%

Genes with transmembrane helices

    1,027

     22.36%

CRISPR repeats

    4

Table 4

Number of genes associated with the general COG functional categories

Code

    value

   %age

      Description

J

    168

   4.7

      Translation, ribosomal structure and biogenesis

A

    3

   0.1

      RNA processing and modification

K

    211

   5.9

      Transcription

L

    276

   7.7

      Replication, recombination and repair

B

    1

   0.0

      Chromatin structure and dynamics

D

    48

   1.3

      Cell cycle control, cell division, chromosome partitioning

Y

    0

   0.0

      Nuclear structure

V

    70

   2.0

      Defense mechanisms

T

    208

   5.8

      Signal transduction mechanisms

M

    266

   7.4

      Cell wall/membrane/envelope biogenesis

N

    56

   1.6

      Cell motility

Z

    0

   0.0

      Cytoskeleton

W

    0

   0.0

      Extracellular structures

U

    102

   2.9

      Intracellular trafficking, secretion, and vesicular transport

O

    162

   4.5

      Posttranslational modification, protein turnover, chaperones

C

    289

   8.1

      Energy production and conversion

G

    127

   3.6

      Carbohydrate transport and metabolism

E

    210

   5.9

      Amino acid transport and metabolism

F

    59

   1.7

      Nucleotide transport and metabolism

H

    143

   4.0

      Coenzyme transport and metabolism

I

    82

   2.3

      Lipid transport and metabolism

P

    196

   5.5

      Inorganic ion transport and metabolism

Q

    58

   1.6

      Secondary metabolites biosynthesis, transport and catabolism

R

    407

   11.4

      General function prediction only

S

    437

   12.2

      Function unknown

-

    1,319

   28.7

      Not in COGs

Insight into the genome sequence

The genomic basis for gliding motility is not yet completely resolved, but the requirement of the genes gldA, gldF and gldG was described [44]. Genes gldA, gldF and gldG exhibit a high degree of sequence similarity to components of ABC transporters [44]. A closer examination of the JP2T genome revealed a region of three genes (Thini_0004.00016790, Thini_0004.00016780, Thini_0004.00016770, currently annotated as ABC-type uncharacterized transport system), for which the derived protein sequences show high similarity to GldA, GldF and GldG of Bdellovibrio bacteriovorus HD100 (Bd1023, Bd1024 and Bd1025) [45]. The requirement of gldA for gliding motility was experimentally shown for Flavobacterium johnsoniae. A non-motile mutant lacking the intact gldA gene was complemented by a vector carrying an intact gldA gene. The motility of the mutant was restored [46].

While we were able to locate a phosphoenolpyruvate carboxylase gene in the genome, (Thini_0004.00035050), we could not identify a gene for malate dehydrogenase. Unless T. nivea encodes a malate dehydrogenase that is not homologous to other malate dehydrogenases, we can not confirm for the neotype strain the genomic basis for the speculation that the original T. nivea culture can fix CO2 as reported by Winogradsky [13] and is a mixotroph [1].

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Anja Frühling (DSMZ) for growing T. nivea cultures. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1.


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References

  1. Larkin JM and Shinabarger DL. Characterization of Thiothrix nivea. Int J Syst Bacteriol. 1983; 33:841-846 View Article
  2. Winogradsky S. Beiträge zur Morphologie und Physiologie der Bakterien. In: Zur Morphologie und Physiologie der Schwefelbakterien. Felix A (ed) Leipzig 1888; 1:1-120.
  3. Rabenhorst L. Flora Europa algarum aquae dulcis et submarinae, sect II. E. Kummer, Leipzig 1865.
  4. Skerman VBD, McGowan V and Sneath PHA. , eds. Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980; 30:225-420 View Article
  5. Larkin JM. Isolation of Thiothrix in pure culture and observation of a filamentous epiphyte on Thiothrix. Curr Microbiol. 1980; 4:155-158 View Article
  6. Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol. 1997; 47:590-592 View ArticlePubMed
  7. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ. Bascic local alignment search tool. J Mol Biol. 1990; 215:403-410PubMed
  8. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P and Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72:5069-5072 View ArticlePubMed
  9. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
  10. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000; 17:540-552PubMed
  11. Lee C, Grasso C and Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002; 18:452-464 View ArticlePubMed
  12. Stamatakis A, Hoover P and Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008; 57:758-771 View ArticlePubMed
  13. Hess PN and De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond. 2007; 92:669-674 View Article
  14. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME and Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci. 2009; 5541:184-200 View Article
  15. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
  16. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM and Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2010; 38:D346-D354 View ArticlePubMed
  17. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ and Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-547 View ArticlePubMed
  18. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today. 2010; 37:9
  19. Woese CR, Kandler O and Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA. 1990; 87:4576-4579 View ArticlePubMed
  20. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
  21. Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, second edition, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York, 2005, p. 1.
  22. Validation list No. 106. Int J Syst Evol Microbiol. 2005; 55:2235-2238 View Article
  23. Garrity GM, Bell JA, Lilburn T. Order V. Thiotrichales ord. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, second edition, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York, 2005, p. 131.
  24. Garrity GM, Bell JA, Lilburn T. Family I. Thiotrichaceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, second edition, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York, 2005, p. 131.
  25. Brock TD. Genus II. Thiothrix Winogradsky 1888, 39. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 119-120.
  26. Howarth R, Unz RF, Seviour EM, Seviour RJ, Blackall LL, Pickup RW, Jones JG, Yaguchi J and Head IM. Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewater-treatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. nov. and Thiothrix defluvii sp. nov. Int J Syst Bacteriol. 1999; 49:1817-1827 View ArticlePubMed
  27. Aruga S, Kamagata Y, Kohno T, Hanada S, Nakamura K and Kanagawa T. Characterization of filamentous Eikelboom type 021N bacteria and description of Thiothrix disciformis sp. nov. and Thiothrix flexilis sp. nov. Int J Syst Evol Microbiol. 2002; 52:1309-1316 View ArticlePubMed
  28. Bland JA and Staley JT. Observations on the biology of Thiothrix. Arch Microbiol. 1978; 117:79-87 View Article
  29. Lackey JB. ELackey EW, Morgan GB. Taxonomy and ecology of the sulfur bacteria. Eng Prog Univ Fla Bull Ser. 1965; 199:3-23
  30. BAuA. 2010, Classification of Bacteria and Archaea in risk groups. TRBA 466, p. 241.Web Site
  31. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS and Eppig JT. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25:25-29 View ArticlePubMed
  32. Larkin JM and Nelson R. Mechanism of attachment of swarm cells ot Thiothrix nivea. J Bacteriol. 1987; 169:5877-5879PubMed
  33. Klenk HP and Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol. 2010; 33:175-182 View ArticlePubMed
  34. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M and Tindall BJ. A phylogeny-driven Genomic Encyclopaedia of Bacteria and Archaea. Nature. 2009; 462:1056-1060 View ArticlePubMed
  35. List of growth media used at DSMZ: Web Site
  36. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG and Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreserv Biobank. 2011; 9:51-55 View Article
  37. . Web Site
  38. Phrap and Phred for Windows. MacOS, Linux, and Unix. Web Site
  39. Zerbino DR and Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-829 View ArticlePubMed
  40. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
  41. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW and Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; 11:119 View ArticlePubMed
  42. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A and Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010; 7:455-457 View ArticlePubMed
  43. Markowitz VM, Ivanova NN, Chen IMA, Chu K and Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009; 25:2271-2278 View ArticlePubMed
  44. McBride MJ. Bacterial gliding motility: Multiple mechanisms for cell movement over surfaces. Annu Rev Microbiol. 2001; 55:49-75 View ArticlePubMed
  45. Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, Keller H, Lambert C, Evans KJ and Goesmann A. A Predator Unmasked: Life Cycle of Bdellovibrio bacteriovorus from a Genomic Perspective. Science. 2004; 303:689-692 View ArticlePubMed
  46. Agarwal S, Hunnicutt DW and McBride MJ. Cloning and characterization of the Flavobacterium johnsoniae (Cytophaga johnsonae) gliding motility gene, gldA. Proc Natl Acad Sci USA. 1997; 94:12139-12144 View ArticlePubMed