Open Access

Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)

  • Hans-Peter Klenk1,
  • Brittany Held2,
  • Susan Lucas3,
  • Alla Lapidus3,
  • Alex Copeland3,
  • Nancy Hammon3,
  • Sam Pitluck3,
  • Lynne A. Goodwin2, 3,
  • Cliff Han2, 3,
  • Roxanne Tapia2, 3,
  • Evelyne-Marie Brambilla1,
  • Gabriele Pötter1,
  • Miriam Land3, 4,
  • Natalia Ivanova3,
  • Manfred Rohde5,
  • Markus Göker1,
  • John C. Detter2, 3,
  • Nikos C. Kyrpides3 and
  • Tanja Woyke3
Standards in Genomic Sciences20126:6020220

DOI: 10.4056/sigs.2635833

Published: 25 May 2012

Abstract

Saccharomonospora azurea Runmao et al. 1987 is a member of the genus Saccharomonospora, which is in the family Pseudonocardiaceae and thus far poorly characterized genomically. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, the surface of peat, and moist and over-heated grain, and may play a role in the primary degradation of plant material by attacking hemicellulose. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for which a completely sequenced type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence with project status ‘Improved high quality draft’, and the annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

Keywords

aerobic chemoheterotrophic Gram-positive vegetative and aerial mycelia spore-forming non-motile soil bacterium Pseudonocardiaceae CSP 2010

Introduction

Strain NA-128T (= DSM 44631 = ATCC 43670 = NBRC 14651) is the type strain of the species Saccharomonospora azurea [1], one of nine species currently in the genus Saccharomonospora [2]. The strain was originally isolated in the course of screening for new antibiotics from a soil sample collected near Guangyun City, Sichuan (China) [1]. The genus name Saccharomonospora was derived from the Greek words for sakchâr, sugar, monos, single or solitary, and spora, a seed or spore, meaning the sugar (-containing) single-spored (organism) [3]. The species epithet was derived from the Latin adjective azurea, azure, referring to the color of the areal mycelium [1]. Yoon et al. [4] showed in 1999 via DNA-DNA hybridization that ‘S. caesia’ [5] (formerly known as ‘Micropolyspora caesia’ [6]), which was not included on the Approved Lists [7], was a synonym of S. azurea. S. azurea and the other type strains of the genus Saccharomonospora were selected for genome sequencing in a DOE Community Sequencing Project (CSP 312) at Joint Genome Institute (JGI), because members of the genus (which originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist and over-heated grain) might play a role in the primary degradation of plant material by attacking hemicellulose. This expectation was underpinned by the results of the analysis of the genome of S. viridis [8], one of the recently sequenced GEBA genomes [9]. The S. viridis genome, the only sequenced genome from the genus Saccharomonospora to date, contained an unusually large number (24) of genes for glycosyl hydrolases (GH) belonging to 14 GH families, which were identified in the Carbon Active Enzyme Database [10]. Hydrolysis of cellulose and starch was also reported for other members of the genus (that are included in CSP 312), such as S. marina [11], S. halophila [12], S. saliphila [13], S. paurometabolica [14], and S. xinjiangensis [15]. Here we present a summary classification and a set of features for S. azurea AN-128T, together with the description of the genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of S. azurea NA-128T was compared using NCBI BLAST [16,17] 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 [18] and the relative frequencies of taxa and keywords (reduced to their stem [19]) were determined, weighted by BLAST scores. The most frequently occurring genera were Saccharomonospora (47.9%), Kocuria (17.7%), Corynebacterium (9.4%), Kibdelosporangium (6.0%) and Prauserella (5.5%) (176 hits in total). Regarding the eight hits to sequences from members of the species, the average identity within HSPs was 99.5%, whereas the average coverage by HSPs was 99.8%. Regarding the 42 hits to sequences from other members of the genus, the average identity within HSPs was 97.0%, whereas the average coverage by HSPs was 98.3%. Among all other species, the one yielding the highest score was Saccharomonospora xinjiangensis (AJ306300), which corresponded to an identity of 98.9% and an HSP coverage of 100.1%. (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 FN667533 ‘stages composting process pilot scale municipal drum compost clone PS3734’, which showed an identity of 100.0% and a HSP coverage of 97.9%. The most frequently occurring keywords within the labels of all environmental samples that produced hits were ‘feedlot’ (7.9%), ‘top’ (4.1%), ‘beef, cattl, coli, escherichia, habitat, marc, neg, pen, primari, secondari, stec, surfac, synecolog’ (3.9%), ‘feedbunk’ (2.3%) and ‘compost’ (1.7%) (74 hits in total). Environmental samples that yielded hits of a higher score than the highest scoring species were not found.

Figure 1 shows the phylogenetic neighborhood of S. azurea in a 16S rRNA based tree. The sequences of the three identical 16S rRNA gene copies in the genome do not differ from the previously published 16S rRNA sequence (Z38017).
Figure 1.

Phylogenetic tree highlighting the position of S. azurea relative to the type strains of the other species within the family Pseudonocardiaceae. The tree was inferred from 1,386 aligned characters [20,21] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [22]. Rooting was done initially using the midpoint method [23] 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 550 ML bootstrap replicates [24] (left) and from 1,000 maximum parsimony bootstrap replicates [25] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [26] are labeled with one asterisk, those also listed as ‘Complete and Published’ with two asterisks [8,27,28]. Actinopolyspora iraqiensis Ruan et al. 1994 was ignored in the tree. The species was proposed to be a later heterotypic synonym of S. halophila [29], although the name A. iraqiensis would have had priority over S. halophila. This taxonomic problem will soon be resolved with regard to the genomes of A. iraqiensis and S. halophila, which were both part of CSP 312.

Cells of S. azurea NA-128T form an irregularly branched vegetative mycelium of 0.3 to 0.4 εm diameter (Figure 2) [1]. The monopodally branching aerial mycelium has a diameter of 0.3 to 0.6 εm [1]; the mature mycelium and the spores are azure to cyaneus when grown on Oatmeal agar (ISP3) or on Czapek sucrose agar [1]. Smooth, round spores are 0.8 to 1.0 mM long, mostly found on the aerial mycelium, but rarely on the substrate mycelium [1]. No distinct soluble pigment was detectable [1]. The growth range of strain NA-128T spans from 24–40°C, with an optimum at 28–37°C [1]. Strain NA-128T grows well in up to 7% NaCl containing medium, but is inhibited at 10% NaCl [1]. Physiological characteristics such as growth substrates, gelatin formation and peptonization of milk are described in detail by Runmao (1987) [1].
Figure 2.

Scanning electron micrograph of S. azurea AN-128T

Chemotaxonomy

The cell wall of strain AN-128T contains meso-diaminopimelic acid. Galactose and arabinose are present, indicating a type IV cell wall / type A whole cell sugar pattern [1]. The fatty acids spectrum is dominated by almost 80% hexadecanoic acids: iso-C16:0 (27.0%), C16:1 cis-9 (17.0%), iso-C16:0 2-OH (14.0%), C16:0 (palmitic acid, 13.0%), iso-C16:1 H (7.0%), anteiso-C16:0 (1.0%) [42]. There are no data available for polar lipids and quinines of this strain.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2010, CSP 312, “Whole genome type strain sequences of the genus Saccharomonospora – a taxonomically troubled genus with bioenergetic potential”. The genome project is deposited in the Genomes On Line Database [26] 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 1.

Classification and general features of S. azurea AN-128 T according to the MIGS recommendations [30].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [31]

 

Phylum Actinobacteria

TAS [32]

 

Class Actinobacteria

TAS [33]

 

Subclass Actinobacteridae

TAS [33,34]

 

Order Actinomycetales

TAS [7,3335]

 

Suborder Pseudonocardineae

TAS [33,34,36]

 

Family Pseudonocardiaceae

TAS [33,34,3638]

 

Genus Saccharomonospora

TAS [7,39]

 

Species Saccharomonospora azurea

TAS [1]

 

Type-strain AN-128

TAS [1]

 

Gram stain

positive

NAS

 

Cell shape

variable

NAS

 

Motility

non-motile

NAS

 

Sporulation

single spores with smooth surface, mainly on aerial mycelium

TAS [1]

 

Temperature range

mesophile, 24–40°C

TAS [1]

 

Optimum temperature

28–37°C

TAS [1]

 

Salinity

grows in up to 7% NaCl; 10% is inhibitory

TAS [1]

MIGS-22

Oxygen requirement

aerobic

TAS [1]

 

Carbon source

mono, di- and trisaccharides

TAS [1]

 

Energy metabolism

chemoheterotrophic

NAS

MIGS-6

Habitat

soil

TAS [1]

MIGS-15

Biotic relationship

free living

NAS

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

TAS [40]

MIGS-23.1

Isolation

soil

TAS [1]

MIGS-4

Geographic location

Guangyuan City, Sichuan (China)

TAS [1]

MIGS-5

Sample collection time

1986 or before

NAS

MIGS-4.1

Latitude

32.45

NAS

MIGS-4.2

Longitude

105.84

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 the Gene Ontology project [41]. 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.

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

1,025.0 × Illumina; 8.6 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.3, Velvet version 1.0.13, phrap version SPS - 4.24

MIGS-32

Gene calling method

Prodigal

 

INSDC ID

AGIU00000000, CM001466

 

GenBank Date of Release

March 6, 2012

 

GOLD ID

Gi07579

 

NCBI project ID

62037

 

Database: IMG

2508501044

MIGS-13

Source material identifier

DSM 44631

 

Project relevance

Bioenergy and phylogenetic diversity

Growth conditions and DNA isolation

Strain NA-128T, DSM 44631, was grown in DSMZ medium 83 (Czapek Peptone Medium) [43] at 28°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 with the following modifications: extended cell lysis time (60 min.) with additional 30µl Achromopeptidase, Lysostaphin, Mutanolysin; proteinase K was applied in 6-fold the supplier recommended amount for 60 min. at 58°C. The purity, quality and size of the bulk gDNA preparation were assessed by JGI according to DOE-JGI guidelines. DNA is available through the DNA Bank Network [44].

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 [45]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 215 contigs in one scaffold was converted into a phrap [46] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (5,162.6 Mb) was assembled with Velvet [47] 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 80.3 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 [46] 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 [45], Dupfinisher [48], or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 158 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [49].

The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 1,033.6 × coverage of the genome. The final assembly contained 345,324 pyrosequence and 64,928,268 Illumina reads.

Genome annotation

Genes were identified using Prodigal [50] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [51]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, 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 [52].

Genome properties

The genome consists of a 4,763,852 bp long chromosome with a 70.1% G+C content (Table 3 and Figure 3). Of the 4,530 genes predicted, 4,472 were protein-coding genes, and 58 RNAs; 96 pseudogenes were also identified. The majority of the protein-coding genes (73.8%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

Graphical map of the chromosome. From left to the right: 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)

4,763,852

100.00%

DNA coding region (bp)

4,287,642

90.00%

DNA G+C content (bp)

3,331,901

70.08%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

4,530

100.00%

RNA genes

58

1.28%

rRNA operons

3

 

tRNA genes

47

1.04%

Protein-coding genes

4,472

98.72%

Pseudo genes

96

2.12%

Genes with function prediction (proteins)

3,342

73.77%

Genes in paralog clusters

2,354

51.96%

Genes assigned to COGs

3,312

73.11%

Genes assigned Pfam domains

3,450

76.16%

Genes with signal peptides

1,332

29.40%

Genes with transmembrane helices

1,070

23.62%

CRISPR repeats

0

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

171

4.6

Translation, ribosomal structure and biogenesis

A

1

0.0

RNA processing and modification

K

394

10.6

Transcription

L

175

4.7

Replication, recombination and repair

B

2

0.1

Chromatin structure and dynamics

D

35

0.9

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

58

1.6

Defense mechanisms

T

190

5.1

Signal transduction mechanisms

M

156

4.2

Cell wall/membrane biogenesis

N

6

0.2

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

36

1.0

Intracellular trafficking and secretion, and vesicular transport

O

134

3.6

Posttranslational modification, protein turnover, chaperones

C

245

6.6

Energy production and conversion

G

259

7.0

Carbohydrate transport and metabolism

E

313

8.4

Amino acid transport and metabolism

F

91

2.4

Nucleotide transport and metabolism

H

194

5.2

Coenzyme transport and metabolism

I

179

4.8

Lipid transport and metabolism

P

176

4.7

Inorganic ion transport and metabolism

Q

152

4.1

Secondary metabolites biosynthesis, transport and catabolism

R

478

12.8

General function prediction only

S

282

7.6

Function unknown

-

1,218

26.9

Not in COGs

Declarations

Acknowledgements

The work conducted by the US Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Authors’ Affiliations

(1)
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
(2)
Bioscience Division, Los Alamos National Laboratory
(3)
DOE Joint Genome Institute
(4)
Oak Ridge National Laboratory
(5)
HZI - Helmholtz Centre for Infection Research

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