Open Access

High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea

  • Imen Nouioui1,
  • Markus Göker2,
  • Lorena Carro1,
  • Maria del Carmen Montero-Calasanz1Email author,
  • Manfred Rohde3,
  • Tanja Woyke4,
  • Nikos C. Kyrpides4, 5 and
  • Hans-Peter Klenk1
Standards in Genomic Sciences201712:4

DOI: 10.1186/s40793-016-0216-0

Received: 1 March 2016

Accepted: 6 December 2016

Published: 6 January 2017

Abstract

Nakamurella lactea DLS-10T , isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10T and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed.

Keywords

Frankineae Rare actinobacteria Nakamurellaceae Bioactive natural product Next generation sequencing

Introduction

The genus Nakamurella , belong to the order Nakamurellales [1] and is one of the rare genera in the class Actinobacteria [2]. The genus Nakamurella is the sole and type genus of the family Nakamurellaceae , which replaced the family Microsphaeraceae [2] in 2004 [3]. The genus and family names were assigned in honour of the microbiologist Kazonuri Nakamura [4].

Only four species with validly published names, Nakamurella multipartita [3, 5], Nakamurella panacisegetis [6, 7], Nakamurella flavida [68], and Nakamurella lactea [6, 7, 9], have been described, and only the genome of Nakamurella multipartita has been published [10].

N. lactea was originally described as Saxeibacter lacteus [9], which was the type species of one of the three genera comprising in the family Nakamurellaceae . Then, in the light of the 16S rRNA gene and rpoB gene sequences similarities and chemotaxonomic features [6], the species was reclassified into the genus Nakamurella . Nakamurella lactea is represented by the type strain DLS-10T (= DSM 19367 T = JCM 16024T = KCTC 19285T ).

The availability of the genome of one more species in the genus will provide vital baseline information for better understanding of the ecology of these rare actinobacteria and their potential as source of bioactive natural products. In the present study, we summarise the phenotypic, physiological and chemotaxonomic, features of N. lactea DLS-10T together with the genomic data.

Organism information

Classification and features

N. lactea DLS-10T was isolated from a rock collected on the parasitic volcano Darangshi Oreum at 300 m above sea level in Jeju island, Republic of Korea (latitude 33.51, longitude 126.52) [9]. It has been shown by Lee et al. [9] and Kim et al. [4, 6] that its cells are aerobic, non-motile, non-spore and non-mycelium forming short rods with 0.4–0.7 μm and 0.9–1.0 μm of cell diameter and length, respectively (Fig. 1), producing cream-coloured colonies on TSA medium. A summary of the classification and general features of N. lactea strain DLS-10T is presented in the Table 1. Additional phenotypic features can be found in Lee et al. and Kim et al. [6, 9].
Fig. 1

Scanning electron micrograph of N. lactea DLS-10T. The bacterium was grown on DSM medium 65 for 3 days at 28C

Table 1

Classification and general features of Nakamurella lactea strain DLS-10T, according to the MIGS recommendations [36] as developed by [22]

MIGS ID

Property

Term

Evidence codea

 

Classification

Domain Bacteria

TAS [39]

  

Phylum Actinobacteria

TAS [40]

  

Class Actinobacteria

TAS [2]

  

Order Nakamurellales

TAS [1]

  

Family Nakamurellaceae

TAS [41]

  

Genus Nakamurella

TAS [3, 41]

  

Species Nakamurella lactea

Type strain DLS-10

TAS [6, 9]

 

Gram stain

Positive

TAS [6, 9]

 

Cell shape

Rod

TAS [6, 9]

 

Motility

non-motile

TAS [6, 9]

 

Sporulation

Non-sporulating

NAS [6, 9]

 

Temperature range

4–37 °C

TAS [6, 9]

 

Optimum temperature

25 °C

TAS [6, 9]

 

pH range

5.1–9.1

TAS [6, 9]

 

pH Optimum

6.0–7.0

 
 

Carbon source

L-Arabinose, myo-inositol and methyl α-D-mannoside, D-cellobiose, D-fructose, D-glucose, D-galactose, lactose, D-maltose, D-mannitol, D-mannose, L-rhamnose, salicin, sucrose and D-trehalose, D- turanose

TAS [6, 9]

MIGS-6

Habitat

Rock

TAS [9]

MIGS-6.3

Salinity

Up to 3% NaCl

TAS [6, 9]

MIGS-22

Oxygen requirement

Aerobic

TAS [9]

MIGS-15

Biotic relationship

free-living

TAS [9]

MIGS-14

Pathogenicity

non-pathogen

NAS

MIGS-4

Geographic location

Korea

TAS [9]

MIGS-5

Sample collection

Not reported

TAS []

MIGS-4.1

Latitude

33.51

TAS [9]

MIGS-4.2

Longitude

126.52

TAS [9]

MIGS-4.4

Altitude

300 m

TAS [9]

aEvidence codes are from of the Gene Ontology project [42]. TAS traceable author statement (i.e., a direct report exists in the literature)

Only four species isolated from soil ( N. panacisegetis and N. flavida ), rock ( N. lactea ) and sludge (N. mutipartita), respectively, are currently classified in the genus. Due to this limited number of the characterised species, the ecological diversity as well as the biotechnological potential of the members of the genus Nakamurella remain to be studied in depth.

Phylogenies based on 16S rRNA gene sequences included in this manuscript were performed using the GGDC web server [11] implementation of the DSMZ phylogenomics pipeline [12]. The multiple alignment was created with MUSCLE [13] and maximum likelihood (ML) and maximum parsimony (MP) trees were inferred from it with RAxML [14] and TNT [15], respectively. For ML, rapid bootstrapping in conjunction with the autoMRE bootstopping criterion [16] and subsequent search for the best tree was used; for MP, 1000 bootstrapping replicates were used in conjunction with tree-bisection-and-reconnection branch swapping and ten random sequence addition replicates. This analysis shows the family Nakamurellaceae [4] as the sister group of the families Cryptosporangiaceae , Sporichthyaceae , and Geodermatophilaceae . The monophyly of the genus Nakamurella was supported by (close to) maximum bootstrap values under ML and MP (Fig. 2).
Fig. 2

Maximum likelihood phylogenetic tree of N. lactea DLS-10T and related type strains within the related families constructed under the GTR + GAMMA model and rooted using Actinomyces bovis NCTC 11535T as outgroup. The branches are scaled in terms of the expected number of substitutions per site (see size bar). Support values from maximum-likelihood (left) and maximum-parsimony (right) bootstrapping are shown above the branches if equal to or larger than 60%

Chemotaxonomic data (optional, Heading 3)

Glucose, mannose, ribose and rhamnose were detected as the whole-cell sugars [5]. The pattern of polar lipid contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, aminophospholipid, five unidentified phosphoglycolipids, and one unidentified glycolipid [6].

The diagnostic peptidoglican is the meso-diaminopimelic acid. The major fatty acids are anteiso-C15:0, C16:0, iso-C16:0, and anteiso-C17:0 [9]. MK-8(H4) and MK-9(H4) are the predominant menaquinones but MK-7(H4) was also revealed in a low amount [6].

Genome sequencing information

Genome project history

N. lactea DLS-10T (DSM 19367 T) was selected for sequencing on the basis of its phylogenetic position [17, 18], and is part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project [19], a follow-up of the Genomic Encyclopedia of Bacteria and Archaea pilot project [20], which aims at increasing the sequencing coverage of key reference microbial genomes and to generate a large genomic basis for the discovery of genes encoding novel enzymes [21]. KMG-I is the first of the production phases of the “Genomic Encyclopedia of Bacteria and Archaea: sequencing a myriad of type strains” initiative [22] and a Genomic Standards Consortium project [23]. The project and the genome sequence are deposited in the Genome OnLine Database [24] and Genbank under the accession number AUFT00000000.1. In Table 2, we summarize genome sequence project.
Table 2

Project information

MIGS ID

Property

Term

MIGS 31

Finishing quality

Level 1: Standard Draft

MIGS-28

Libraries used

NOHX

MIGS 29

Sequencing platforms

Illumina, Illumina HiSeq 2000

MIGS 31.2

Fold coverage

NA

MIGS 30

Assemblers

Allpaths/Velvet

MIGS 32

Gene calling method

Prodigal 2.5

 

Locus Tag

K340

 

Genbank ID

AUFT00000000.1

 

GenBank Date of Release

2013-06-03

 

GOLD ID

Gi11889

 

BIOPROJECT

PRJNA195807

MIGS 13

Source Material Identifier

DSM 19367T

 

Project relevance

GEBA-KMG, Tree of Life

Growth conditions and genomic DNA preparation

A N. lactea DLS-10T culture was prepared in DSM medium 65 [25] at 28 °C. Genomic DNA was extracted using MasterPure™ Gram Positive DNA Purification Kit (Epicentre MGP04100) following the standard protocol provided by the manufacturer but modified by the incubation on ice overnight on a shaker, the use of additional 1 μl proteinase K, and the addition of 7.5 units achromopeptidase, 7.5 μg/μl lysostaphine, 1050.0 units lysozyme, and 7.5 units mutanolysine. DNA is available from DSMZ through the DNA Bank Network [26].

Genome sequencing and assembly

The draft genome of N. lactea DLS-10T was generated at the DOE Joint genome Institute (JGI) using the Illumina technology [27]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform, which generated 13,910,936 reads totalling 2,086.6 Mb. All general aspects of library construction and sequencing performed at the JGI can be found at http://www.jgi.doe.gov. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artefacts (unpublished results). Following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet (version 1.1.04) [28], (2) 1–3 kb simulated paired end reads were created from Velvet contigs using wgsim (https://github.com/lh3/wgsim), (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG (version r42328) [29]. Parameters for assembly steps were: 1) Velvet (velveth:63 –shortPaired and velvetg: −very clean yes –exportFiltered yes –min contig lgth 500 –scaffolding no–cov cutoff 10) 2) wgsim (−e 0 –1 100 –2 100 –r 0 –R 0 –X 0) 3) Allpaths–LG (PrepareAllpathsInputs:PHRED 64 = 1 PLOIDY = 1 FRAG COVERAGE = 125 JUMP COVERAGE = 25 LONG JUMP COV = 50, RunAllpathsLG: THREADS = 8 RUN = std shredpairs TARGETS = standard VAPI WARN ONLY = True OVERWRITE = True). The final draft assembly contained 31 contigs in 27 scaffolds. The total size of the genome is 5.8 Mb and the final assembly is based on 712.8 Mb of Illumina data, which provides an average 122.5X coverage of the genome.

Genome annotation

The complete genome sequence was annotated using the JGI Prokaryotic Automatic Annotation Pipeline [30] with additional manual review using the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [31]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non redundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. The tRNAScanSE tool [32] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [33]. Other non–coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL [34]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG) platform [35, 36] developed by the Joint Genome Institute, Walnut Creek, CA, USA [37].

Genome properties

The 5820860 bp of genome size of N. lactea DLS-10T presents 5100 protein-coding genes, 3 rRNA genes (5S, 16S, 23S RNA) and 59 tRNA genes. A G + C content of 68.9% was calculated. More genome details are listed in Tables 3 and 4.
Table 3

Genome statistics

Attribute

Value

% of Total

Genome size (bp)

5820860

100.00

DNA coding (bp)

5332245

91.61

DNA G + C (bp)

4011790

68.92

DNA scaffolds

27

100.00

Total genes

5169

100.00

Protein coding genes

5100

98.67

RNA genes

69

1.33

Pseudo genes

231

 

Genes in internal clusters

588

11.38

Genes with function prediction

4048

78.31

Genes assigned to COGs

3321

64.25

Genes with Pfam domains

4211

81.47

Genes with signal peptides

432

8.36

Genes with transmembrane helices

1206

23.33

CRISPR repeats

1

 
Table 4

Number of genes associated with general COG functional categories

Code

Value

%

Description

J

198

5.07

Translation, ribosomal structure and biogenesis

A

1

0.03

RNA processing and modification

K

392

10.04

Transcription

L

122

3.12

Replication, recombination and repair

B

1

0.03

Chromatin structure and dynamics

D

25

0.64

Cell cycle control, Cell division, chromosome partitioning

V

94

2.41

Defence mechanisms

T

137

3.51

Signal transduction mechanisms

M

144

3.69

Cell wall/membrane biogenesis

N

10

0.26

Cell motility

U

23

0.59

Intracellular trafficking and secretion

O

121

3.1

Posttranslational modification, protein turnover, chaperones

C

210

5.38

Energy production and conversion

G

648

12.31

Carbohydrate transport and metabolism

E

459

11.75

Amino acid transport and metabolism

F

91

2.33

Nucleotide transport and metabolism

H

219

5.61

Coenzyme transport and metabolism

I

255

6.53

Lipid transport and metabolism

P

244

6.25

Inorganic ion transport and metabolism

Q

154

3.94

Secondary metabolites biosynthesis, transport and catabolism

R

443

11.34

General function prediction only

S

158

44.05

Function unknown

-

1848

35.75

Not in COGs

Conclusion

The genome of N. lactea will be used to study, for the first time, its potential as bioactive natural products source and the correlation between the rare soil bacteria and their habitat. According to [38], the within-species deviation in genomic G + C content is at most 1%. The range of 70.4–74.3% given in by Kim et al. [6] is thus too broad and too deviating from the 68.9% calculated in the genome sequence, much like the value 74.3% provided by Lee et al. [9]. This calls for an emendation of the species description [38].

Emended description of Nakamurella lactea (Lee et al. [9]) Kim et al. [6]

The properties are as given in the species description by Kim et al. [6] with the following emendation. Based on the genomic data the G + C content is 68.9%.

Declarations

Acknowledgements

We thank Katja Steenblock (DSMZ) for her help in preparing the culture of N. lactea DSM 19367 T and Evelyne Brambilla (DSMZ) for her contribution in the DNA extraction. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231.

Authors’ contributions

IN and HPK conceived of the study and participated in its design and coordination. IN, LC and MCMC collaborated in acquisition of data, analysis of them and drafted the manuscript. MG and RM performed the phylogenetic analysis and SEM images, respectively. TW and NCK participated in genome sequencing, annotation and analysis. All authors contributed in improving the quality of the manuscript and approved the final version.

Competing interests

The authors declare that they have no competing interests.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
School of Biology, Newcastle University
(2)
Leibniz Institute DSMZ
(3)
Central Facility for Microscopy, HZI—Helmholtz Centre for Infection Research
(4)
Department of Energy Joint Genome Institute
(5)
Department of Biological Sciences, Faculty of Science, King Abdulaziz University

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Copyright

© The Author(s). 2017