Open Access

Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417

  • Wayne Reeve1Email author,
  • Jason Terpolilli1,
  • Vanessa Melino1,
  • Julie Ardley1,
  • Rui Tian1,
  • Sofie De Meyer1,
  • Ravi Tiwari1,
  • Ronald Yates1, 2,
  • Graham O’Hara1,
  • John Howieson1,
  • Mohamed Ninawi1,
  • Hazuki Teshima3,
  • David Bruce3,
  • Chris Detter3,
  • Roxanne Tapia3,
  • Cliff Han3,
  • Chia-Lin Wei3,
  • Marcel Huntemann3,
  • James Han3,
  • I-Min Chen4,
  • Konstantinos Mavrommatis3,
  • Victor Markowitz4,
  • Natalia Ivanova3,
  • Galina Ovchinnikova3,
  • Ioanna Pagani3,
  • Amrita Pati3,
  • Lynne Goodwin5,
  • Lin Peters3,
  • Tanja Woyke3 and
  • Nikos Kyrpides3
Standards in Genomic Sciences20139:9020273

https://doi.org/10.4056/sigs.4518260

Published: 20 December 2013

Abstract

Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this microsymbiont is a poorly effective N2 fixer with the legume host Lupinus angustifolius L.; a lupin species of considerable economic importance in both Chile and Australia. The symbiosis formed with L. angustifolius produces less than half of the dry matter achieved by the symbioses with commercial inoculant strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an important candidate strain with which to investigate the genetics of effective N2 fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of Bradyrhizobium sp. strain WSM1417, together with genome sequence information and annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

Keywords

root-nodule bacteria nitrogen fixation rhizobia Alphaproteobacteria

Introduction

The Fabaceae plant family is the third largest family of flowering plants with a unique ecological role in nitrogen (N2) fixation. This family encompasses the three subfamilies Caesalpinioideae, Mimosoideae, and Faboideae (or Papilionoideae). The legume genus Lupinus (commonly known as lupin) consists of around 280 species classified within the Genisteae tribe of the subfamily Faboideae with major centers of diversity in South and Western North America, the Andes, the Mediterranean regions, and Africa. This legume has been grown in rotations with cereals for at least 2000 years [1] and is widely distributed within the old and new worlds [2]. The grain may be easily harvested and contains the full range of essential amino acids, and because of its high concentration of sulfur containing amino acids has high feed value for stock [2].

The lupin root nodule bacteria have all been classified within the genus Bradyrhizobium [3,4] with the exception of Microvirga lupini that was found to nodulate with Lupinus texensis [5]. Bradyrhizobium spp. are commonly associated with the nodulation of sub-tropical and tropical legumes such as soybean [6,7]. In contrast, lupins are the only agricultural grain legume nodulated by this genus in Mediterranean-type climatic zones. Strains of lupin-nodulating Bradyrhizobium are also able to nodulate the herbaceous Mediterranean legume Ornithopus (seradella) spp. In this context, lupin Bradyrhizobium strains are rare microsymbionts of herbaceous and crop legumes endemic to the cool climatic regions of the world.

The cultivation of lupin in these regions provides a cash crop alternative to soy. Lupinus angustifolius in particular has been extensively used to extend grain production into poor quality soils without fertilizer supplementation since fixed nitrogen can be obtained from the symbiosis with Bradyrhizobium [8]. Considerable variation exists in the amount of N2 fixed in the lupin-Bradyrhizobium association [8]. This is significant in agricultural ecosystems, as the benefits derived from growing lupins accrue both to the grain produced and the N2 fixed [9]. A well-grown lupin crop may fix up to 300 kg of N per ha. It is therefore important to understand the genetic constraints to optimal N2 fixation in this symbiosis. Bradyrhizobium sp. strain WSM1417 represents the lower end of the scale in strain N2 fixation capacity on L. angustifolius, and hence its genome sequence presents an opportunity to understand the genetic elements responsible for this trait. Here we present a summary classification and a set of general features for Bradyrhizobium sp. WSM1417 together with the description of the complete genome sequence and its annotation.

Classification and general features

Bradyrhizobium sp. WSM1417 is a motile, Gram-negative, non-spore-forming rod (Figure 1 Left and Center) in the order Rhizobiales of the class Alphaproteobacteria. It is slow growing in laboratory culture, forming 1–2mm colonies within 7–10 days when grown on half Lupin Agar (½LA) [10] at 28°C. Colonies on ½LA are white-opaque, slightly domed, moderately mucoid with smooth margins (Figure 1C). Minimum Information about the Genome Sequence (MIGS) is provided in Table 1. Figure 2 shows the phylogenetic neighborhood of Bradyrhizobium sp. strain WSM1417 in a 16S rRNA sequence based tree. This strain clusters closest to Bradyrhizobium canariense LMG 22265T and Bradyrhizobium japonicum LMG 6138T with 99.85% and 99.48% sequence identity, respectively.
Figure 1.

Images of Bradyrhizobium sp strain WSM1417 using scanning (Left) and transmission (Center) electron microscopy as well as light microscopy to visualize colony morphology on a solid medium (Right).

Figure 2.

Phylogenetic tree showing the relationships of Bradyrhizobium sp. strain WSM1417 (shown in blue print) with some of the root nodule bacteria in the order Rhizobiales based on aligned sequences of the 16S rRNA gene (1,334 bp internal region). All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA, version 5.05 [20]. The tree was built using the maximum likelihood method with the General Time Reversible model. Bootstrap analysis [21] with 500 replicates was performed to assess the support of the clusters. Type strains are indicated with a superscript T. Strains with a genome sequencing project registered in GOLD [22] are in bold print and the GOLD ID is mentioned after the accession number. Published genomes are designated with an asterisk.

Table 1.

Classification and general features of Bradyrhizobium sp. strain WSM1417 according to the MIGS recommendations [11,12].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [12]

 

Phylum Proteobacteria

TAS [13]

 

Class Alphaproteobacteria

TAS [4,14]

 

Order Rhizobiales

TAS [14,15]

 

Family Bradyrhizobiaceae

TAS [14,16]

 

Genus Bradyrhizobium

TAS [17]

 

Species Bradyrhizobium sp.

IDA

 

Gram stain

Negative

IDA

 

Cell shape

Rod

IDA

 

Motility

Motile

IDA

 

Sporulation

Non-sporulating

NAS

 

Temperature range

Mesophile

NAS

 

Optimum temperature

28°C

NAS

 

Salinity

Not reported

 

MIGS-22

Oxygen requirement

Aerobic

NAS

 

Carbon source

Varied

IDA

 

Energy source

Chemoorganotroph

NAS

MIGS-6

Habitat

Soil, root nodule, host

IDA

MIGS-15

Biotic relationship

Free living, symbiotic

IDA

MIGS-14

Pathogenicity

Non-pathogenic

NAS

 

Biosafety level

1

TAS [18]

 

Isolation

Root nodule

IDA

MIGS-4

Geographic location

Papudo, Chile

IDA

MIGS-5

Nodule collection date

1995

IDA

MIGS-4.1

Longitude

−71.452814

IDA

MIGS-4.2

Latitude

−32.521849

IDA

MIGS-4.3

Depth

Not recorded

 

MIGS-4.4

Altitude

Not recorded

 

Evidence codes — IDA: Inferred from Direct Assay (i.e. first time published); 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 [19].

Symbiotaxonomy

Bradyrhizobium sp. WSM1417 is poorly effective on L. angustifolius, producing only 45% of the dry matter compared to that achieved by the commercial inoculant strain Bradyrhizobium sp. WSM471 on this species. In contrast on L. mutabilis, WSM1417 performs much better, yielding 83% of the dry matter produced by WSM471 on this same host.

Genome sequencing and annotation information

Genome project history

This organism was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the Community Sequencing Program at the U.S. Department of Energy, Joint Genome Institute (JGI) for projects of relevance to agency missions. The genome project is deposited in the Genomes OnLine Database [22] and an improved-high-quality-draft genome sequence in IMG. Sequencing, finishing and annotation were performed by the JGI. A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information for Bradyrhizobium sp. strain WSM1417.

MIGS ID

Property

Term

MIGS-31

Finishing quality

Improved high-quality draft

MIGS-28

Libraries used

Illumina GAii shotgun and paired end 454 libraries

MIGS-29

Sequencing platforms

Illumina GAii and454 GS FLX Titanium technologies

MIGS-31.2

Sequencing coverage

8.1× 454 paired end

MIGS-30

Assemblers

Velvet 1.0.13, Newbler 2.3, phrap 4.24

MIGS-32

Gene calling methods

Prodigal 1.4, GenePRIMP

 

GOLD ID

Gi06490

 

NCBI project ID

61989

 

Database: IMG

2507262055

 

Project relevance

Symbiotic N2 fixation, agriculture

Growth conditions and DNA isolation

Bradyrhizobium sp. strain WSM1417 was grown to mid logarithmic phase in TY rich medium [23] on a gyratory shaker at 28°C. DNA was isolated from 60 mL of cells using a CTAB (Cetyltrimethylammonium bromide) bacterial genomic DNA isolation method [24].

Genome sequencing and assembly

The genome of Bradyrhizobium sp. strain WSM1417 was sequenced at the Joint Genome Institute (JGI) using a combination of Illumina [25] and 454 technologies [26]. An Illumina GAii shotgun library which generated 82,690,654 reads totaling 6,284.5 Mb, and a paired end 454 library with an average insert size of 10 kb which generated 770,255 reads totaling 144.4 Mb of 454 data were generated for this genome. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website [24]. The initial draft assembly contained 2 contigs in 1 scaffold. The 454 paired end data was assembled with Newbler, version 2.3. The Newbler consensus sequences were computationally shredded into 2 kb overlapping fake reads (shreds). Illumina sequencing data were assembled with Velvet, version 1.0.13 [27], and the consensus sequences were computationally shredded into 1.5 kb overlapping fake reads (shreds). We integrated the 454 Newbler consensus shreds, the Illumina Velvet consensus shreds and the read pairs in the 454 paired end library using parallel phrap, version SPS - 4.24 (High Performance Software, LLC). The software Consed (Ewing and Green 1998; Ewing et al. 1998; Gordon et al. 1998) was used in the following finishing process. Illumina data was used to correct potential base errors and increase consensus quality using the software Polisher developed at JGI (Alla Lapidus, unpublished). Possible mis-assemblies were corrected using gapResolution (Cliff Han, unpublished), Dupfinisher (Han, 2006), or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR (J-F Cheng, unpublished) primer walks. A total of 126 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. The estimated genome size is 8.1 Mb and the final assembly is based on 65.8 Mb of 454 draft data, which provides an average 8.1× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [28] as part of the DOE-JGI Annotation pipeline [29], followed by a round of manual curation using the JGI GenePRIMP pipeline [30]. 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. These data sources were combined to assert a product description for each predicted protein. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [31], RNAMMer [32], Rfam [33], TMHMM [34], and SignalP [35]. Additional gene prediction analyses and functional annotation were performed within the Integrated Microbial Genomes (IMG-ER) platform [24,36].

Genome properties

The genome is 8,048,963 nucleotides with 63.16% GC content (Table 3) and comprised of a single scaffold of two contigs. From a total of 7,772 genes, 7,695were protein encoding and 77 RNA only encoding genes. Within the genome, 272 pseudogenes were also identified. The majority of genes (74.03%) were assigned a putative function whilst the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 4 and Figure 3.
Figure 3.

Graphical circular map of the chromosome of Bradyrhizobium sp. strain WSM1417. From outside to the center: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Table 3.

Genome statistics for Bradyrhizobium sp. strain WSM1417.

Attribute

Value

% of Total

Genome size (bp)

8,048,963

100.00

DNA coding region (bp)

6,769,978

84.11

DNA G+C content (bp)

5,084,093

63.16

Number of scaffolds

1

 

Number of contigs

2

 

Total genes

7,772

100.00

RNA genes

77

0.99

rRNA operons

1

 

Protein-coding genes

7,695

99.01

Genes with function prediction

5,754

74.03

Genes assigned to COGs

5,704

73.39

Genes assigned Pfam domains

6,011

77.34

Genes with signal peptides

872

11.22

Genes with transmembrane helices

1,826

23.49

CRISPR repeats

0

 
Table 4.

Number of protein coding genes of Bradyrhizobium sp. WSM1417 associated with the general COG functional categories.

Code

Value

%age

COG Category

J

202

3.15

Translation, ribosomal structure and biogenesis

A

3

0.05

RNA processing and modification

K

430

6.71

Transcription

L

283

4.42

Replication, recombination and repair

B

2

0.03

Chromatin structure and dynamics

D

37

0.58

Cell cycle control, mitosis and meiosis

Y

0

0.00

Nuclear structure

V

90

1.40

Defense mechanisms

T

354

5.53

Signal transduction mechanisms

M

315

4.92

Cell wall/membrane biogenesis

N

130

2.03

Cell motility

Z

1

0.02

Cytoskeleton

W

0

0.00

Extracellular structures

U

138

2.15

Intracellular trafficking and secretion

O

210

3.28

Posttranslational modification, protein turnover, chaperones

C

417

6.51

Energy production conversion

G

431

6.73

Carbohydrate transport and metabolism

E

678

10.58

Amino acid transport metabolism

F

90

1.40

Nucleotide transport and metabolism

H

235

3.67

Coenzyme transport and metabolism

I

332

5.18

Lipid transport and metabolism

P

331

5.17

Inorganic ion transport and metabolism

Q

244

3.81

Secondary metabolite biosynthesis, transport and catabolism

R

793

12.38

General function prediction only

S

660

10.30

Function unknown

-

2,068

26.61

Not in COGS

Declarations

Acknowledgements

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. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi’s PhD project.

Authors’ Affiliations

(1)
Centre for Rhizobium Studies, Murdoch University
(2)
Department of Agriculture and Food
(3)
DOE Joint Genome Institute
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Bioscience Division, Los Alamos National Laboratory

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Copyright

© The Author(s) 2013