Open Access

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)

  • Konstantinos Mavromatis1,
  • Johannes Sikorski2,
  • Alla Lapidus1,
  • Tijana Glavina Del Rio1,
  • Alex Copeland1,
  • Hope Tice1,
  • Jan-Fang Cheng1,
  • Susan Lucas1,
  • Feng Chen1,
  • Matt Nolan1,
  • David Bruce1, 3,
  • Lynne Goodwin1, 3,
  • Sam Pitluck1,
  • Natalia Ivanova1,
  • Galina Ovchinnikova1,
  • Amrita Pati1,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Miriam Land1, 5,
  • Loren Hauser1, 5,
  • Yun-Juan Chang1, 5,
  • Cynthia D. Jeffries1, 5,
  • Patrick Chain1, 3,
  • Linda Meincke1, 3,
  • David Sims1, 3,
  • Olga Chertkov1, 3,
  • Cliff Han1, 3,
  • Thomas Brettin1, 3,
  • John C. Detter1, 3,
  • Claudia Wahrenburg2,
  • Manfred Rohde6,
  • Rüdiger Pukall2,
  • Markus Göker2,
  • Jim Bristow1,
  • Jonathan A. Eisen1, 7,
  • Victor Markowitz4,
  • Philip Hugenholtz1,
  • Hans-Peter Klenk2 and
  • Nikos C. Kyrpides1
Standards in Genomic Sciences20102:2010009

DOI: 10.4056/sigs.591104

Published: 28 February 2010

Abstract

Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘Alicyclobacillaceae’. A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family ‘Alicyclobacillaceae’. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

thermophile acidophilic aerobic non-pathogenic food spoilage non-motile but encodes flagellar genes GEBA

Introduction

Strain 104-IAT (= DSM 446 = ATCC 27009 = JCM 5260 = NCIMB 11725) is the type strain of the species Alicyclobacillus acidocaldarius, which is the type species of the genus Alicyclobacillus [1]. The genus currently consists of 20 species and two subspecies. Strain 104-IAT was originally isolated as ‘Bacillus acidocaldarius’ in 1971 (or earlier) from a hot and acidic spring in Yellowstone National Park, USA. In 1992, it was reclassified on the basis of comparative 16S rRNA gene sequence analysis into the new genus Alicyclobacillus [1]. With the description of A. acidocaldarius subsp. rittmannii in 2002 [2] the subspecies name A. acidocaldarius subsp. acidocaldarius was automatically created following rule 46 of the bacteriological code [3], with 104-IAT as its type strain. (hereinafter nevertheless referred to as A. acidocaldarius, without subspecies epithet). The species name derives from ‘acidus’ from Latin meaning acidic combined with ‘caldarius’, Latin for ‘belonging to the hot’. Due to its thermoacidic nature, this species serves as a model organism for molecular and biochemical studies of its enzymes [419]. Strain 104-IAT has also been used to produce the restriction enzyme BacI [20]. Here we present a summary classification and a set of features for A. acidocaldarius 104-IAT, together with the description of the complete genomic sequencing and annotation.

Classification and features

The type strain 104-IAT and several other strains were isolated from acidic hot springs in the Yellowstone National Park, USA, from soil from an acid fumarole in the Hawaiian Volcano National Park [21], and also from acidic environments in Japan [22]. Other strains, as identified by 16S rRNA gene sequences and by metabolic traits, were isolated from orchard soil, mango juice, vinegar flies or pre-pasteurized pear puree in South Africa [2325]. These findings are supported by the experimentally determined heat resistance of A. acidocaldarius strains in water, acidic buffer and orange juice [26]. Thus, A. acidocaldarius might be involved in food and fruit spoilage, which is a characteristic of several other species of the genus Alicyclobacillus [2325,27]. Clones with high sequence similarity (99%, AB042056) with the 16S rRNA gene sequence of strain 104-IAT are reported by the NCBI BLAST server from a ‘simulated low level waste site’ in USA (GQ263212), but not with any metagenomic environmental samples (October 2009).

Figure 1 shows the phylogenetic neighborhood of for A. acidocaldarius 104-IAT in a 16S rRNA based tree. The sequences of the six 16S rRNA gene copies in the genome of A. acidocaldarius 104-IAT, differ from each other by up to six nucleotides, and differ by up to five nucleotides from the previously published 16S rRNA sequence derived from DSM 446 (AJ496806).
Figure 1.

Phylogenetic tree highlighting the position of A. acidocaldarius 104-IAT relative to the other type strains within the family. The tree was inferred from 1,419 aligned characters [28,29] of the 16S rRNA gene sequence under the maximum likelihood criterion [30] and rooted with the genus Sulfobacillus. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [31] are shown in blue, published genomes in bold.

On B. acidocaldarius medium (BAM medium) [32] strain 104-IAT forms round, slightly mucous, creamy-white colonies after 72 hours of growth with a diameter of 1–4 mm and rod shaped cells that were 2.0–4.5 µm long and 0.5–1.0 µm wide (Table 1 and Figure 2) [22]. The endospores are terminal or subterminal and the sporangia are not swollen [22]. The upper and lower pH growth limits are pH 2 and pH 6 [21]. Strain 104-IAT grows on basal medium supplemented with glucose, galactose, casamino acids, starch, glycerol, sucrose, gluconate, inositol, ribose, rhamnose, and lactose, but not with ethanol, sorbitol, sodium acetate, succinic acid, and sodium citrate [21]. Strain 104-IAT hydrolyses gelatin and starch but is oxidase negative and does not reduce nitrate to nitrite [43]. Strain 104-IAT produces acid from glycerol, L-arabinose, D-xylose, D-galactose, rhamnose, mannitol, methyl-α-D-glucoside, arbutin, aesculin, salicin, cellobiose, maltose, lactose, melibiose, sucrose, trehalose, D-raffinose, starch, and glycogen, but it does not produce acid from erythritol, D-arabinose, L-xylose, L-sorbose, inositol, sorbitol, methyl-α-D-mannisode, amygdalin, melezitose, xylitol, β-gentibiose, D-turanose, D-lyxose, D-tagatose, D-fucose, and 5-ketogluconate [43]. These acid production characteristics are largely congruent with the results from [22], however, L-sorbose, salicin, D-raffinose, starch, and D-turanose deviate across the studies [22,43].
Figure 2.

Scanning electron micrograph of A. acidocaldarius 104-IAT

Table 1.

Classification and general features of A. acidocaldarius 104-IAT in accordance with the MIGS recommendations [33]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [34]

 

Phylum Firmicutes

TAS [3537]

 

Class Bacilli

TAS [36]

 

Order Bacillales

TAS [38,39]

 

Family ‘Alicyclobacillaceae

TAS [40]

 

Genus Alicyclobacillus

TAS [1]

 

Species Alicyclobacillus acidocaldarius

TAS [21]

 

Type strain 104-IA

TAS [21]

 

Gram stain

positive

TAS [21]

 

Cell shape

small rods

TAS [1]

 

Motility

not reported (relevant genes missing)

NAS

 

Sporulation

refractile endospores

TAS [21]

 

Temperature range

45°C−70°C

TAS [21]

 

Optimum temperature

60°C−65°C

TAS [21]

 

Salinity

does not grow with 5% (w/v) NaCl

TAS [22]

MIGS-22

Oxygen requirement

strictly aerobic

TAS [21]

 

Carbon source

saccharolytic

TAS [21]

 

Energy source

carbohydrates

TAS [21]

MIGS-6

Habitat

hot acidic springs and soil

TAS [21]

MIGS-15

Biotic relationship

free living

NAS

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

TAS [41]

 

Isolation

acid hot spring

TAS [21]

MIGS-4

Geographic location

Nymph Creek, Yellowstone National Park, USA

TAS [21]

MIGS-5

Sample collection time

about 1970

TAS [21]

MIGS-4.1

Latitude

44.376

NAS

MIGS-4.2

Longitude

110.690

NAS

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

not reported

 

Evidence codes - IDA: Inferred from Direct Assay (first time in publication); 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 [42]. If the evidence code is IDA, then the property was directly observed for a living isolate by one of the authors or an expert mentioned in the acknowledgements.

Motility has not been reported for strain 104-IAT, although closely related species from the genus Alicyclobacillus are motile [22,27,4345], which suggests a recent loss of motility in A. acidocaldarius. Indeed, strain 104-IAT appears to have all genes necessary for a flagellum. However, essential genes for type 3 secretion system chaperones (flgN, fliJ, fliT) and for flagellar gene expression (flhC, flhD) are missing in the genome, which finally explains the non-motile phenotype.

Chemotaxonomy

Characteristic for several Alicyclobacillus species is the presence of a large amount of ω-alicyclic fatty acids [1,46]. As such, strain 104-IAT has approximately 51 ω-cyclohexane C17:0 and 33% ω-cyclohexane C19:0. Other fatty acids such as C16:0, C18:0, iso-C15:0, iso-C16:0, iso-C18:0, anteiso-C15:0, and anteiso-C17:0 amount at individual levels of approximately 1% to 5% [22,43]. Fatty acid composition is rather stable though not static across different temperature and pH values [47]. Moreover, strain 104-IAT produces hopanoids, a group of pentacyclic triterpenoids, which together with the fatty acids constitute the lipophilic core of the cytoplasmic membrane. The amount of hopanoids depends on the temperature more so than the pH value [48]. The main isoprenoid quinone is menaquinone with seven isoprene units (MK-7) [1].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genome OnLine Database [31] 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

Finished

MIGS-28

Libraries used

One Sanger 8 kb pMCL200 library and one 454 pyrosequencing standard library

MIGS-29

Sequencing platforms

ABI3730, 454 GS FLX

MIGS-31.2

Sequencing coverage

7.0× Sanger; 27.3× pyrosequencing

MIGS-30

Assemblers

Newbler, Phrap

MIGS-32

Gene calling method

Prodigal, GenePRIMP

 

INSDC ID

CP001727 (chromosome)

  

CP001728-30 (plasmids)

 

GenBank Date of Release

September 10–14, 2009

 

GOLD ID

Gc01110

 

NCBI project ID

29405

 

Database: IMG-GEBA

2501939636

MIGS-13

Source material identifier

DSM 446

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

A. acidocaldarius 104-IAT, DSM 446, was grown in DSM Medium 402 [49] at 60°C. DNA was isolated from 0.5–1 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) with cell lysis modification st/L [50] and one hour incubation at 37°C.

Genome sequencing and assembly

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov/. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 3,478 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher [51] or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 767 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in 100,000. The final assembly contains 24,980 Sanger and 363,136 Pyrosequencing reads. Together all sequence types provided 34.3 × coverage of the genome

Genome annotation

Genes were identified using Prodigal [52] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [53]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and manual functional annotation were performed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform [54].

Genome properties

The genome consists of a 3,018,755 bp long chromosome and three plasmids of 91,726 bp, 87,298 bp, and 7,907 bp (Table 3 and Figure 3). Of the 3,235 genes predicted, 3,153 were protein-coding genes, and 82 RNAs; 69 pseudogenes were also identified. The majority of the protein-coding genes (68.4%) were assigned with a putative function while those remaining were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

Graphical circular map of the chromosome and plasmids. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

3,205,686

100.00%

DNA coding region (bp)

2,907,874

90.71%

DNA G+C content (bp)

1,984,066

61.89%

Number of replicons

4

 

Extrachromosomal elements

3

 

Total genes

3,235

100.00%

RNA genes

82

2.53%

rRNA operons

6

 

Protein-coding genes

3,153

97.47%

Pseudo genes

82

2.13%

Genes with function prediction

2,214

68,44%

Genes in paralog clusters

661

20.43%

Genes assigned to COGs

2,221

68.66%

Genes assigned Pfam domains

2,297

71.00%

Genes with signal peptides

686

21.21%

Genes with transmembrane helices

858

26.52%

CRISPR repeats

4

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

147

4.7

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

191

6.1

Transcription

L

177

5.6

Replication, recombination and repair

B

0

0.0

Chromatin structure and dynamics

D

33

1.0

Cell cycle control, mitosis and meiosis

Y

0

0.0

Nuclear structure

V

29

0.9

Defense mechanisms

T

110

3.5

Signal transduction mechanisms

M

124

3.9

Cell wall/membrane biogenesis

N

58

1.8

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

59

1.9

Intracellular trafficking and secretion

O

78

2.5

Posttranslational modification, protein turnover, chaperones

C

130

4.1

Energy production and conversion

G

203

6.4

Carbohydrate transport and metabolism

E

201

6.4

Amino acid transport and metabolism

F

61

1.9

Nucleotide transport and metabolism

H

117

3.7

Coenzyme transport and metabolism

I

120

3.8

Lipid transport and metabolism

P

104

3.3

Inorganic ion transport and metabolism

Q

58

1.8

Secondary metabolites biosynthesis, transport and catabolism

R

266

8.4

General function prediction only

S

185

5.9

Function unknown

-

1014

32.2

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy’s 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, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(3)
Bioscience Division, Los Alamos National Laboratory
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Oak Ridge National Laboratory
(6)
HZI - Helmholtz Center for Infection Research
(7)
University of California Davis Genome Center

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