Open Access

Complete genome sequence of Mesorhizobium australicum type strain (WSM2073T)

  • Wayne Reeve1Email author,
  • Kemanthi Nandasena1,
  • Ron Yates1, 5,
  • Ravi Tiwari1,
  • Graham O’Hara1,
  • Mohamed Ninawi1,
  • Wei Gu2,
  • Lynne Goodwin2,
  • Chris Detter2,
  • Roxanne Tapia2,
  • Cliff Han2,
  • Alex Copeland3,
  • Konstantinos Liolios3,
  • Amy Chen4,
  • Victor Markowitz4,
  • Amrita Pati3,
  • Konstantinos Mavromatis3,
  • Tanja Woyke3,
  • Nikos Kyrpides3,
  • Natalia Ivanova3 and
  • John Howieson1
Standards in Genomic Sciences20139:9020410

DOI: 10.4056/sigs.4568282

Published: 20 December 2013

Abstract

Mesorhizobium australicum strain WSM2073T was isolated from root nodules on the pasture legume Biserrula pelecinus growing in Australia in 2000. This aerobic, motile, gram negative, non-spore-forming rod is poorly effective in N2 fixation on B. pelecinus and has gained the ability to nodulate B. pelecinus following in situ lateral transfer of a symbiosis island from the original inoculant strain for this legume, Mesorhizobium ciceri bv. biserrulae WSM1271. We describe that the genome size of M. australicum strain WSM2073T is 6,200,534 bp encoding 6,013 protein-coding genes and 67 RNA-only encoding genes. This genome does not contain any plasmids but has a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.

Keywords

root-nodule bacteria nitrogen fixation evolution lateral transfer of genes integrative and conjugative elements symbiosis Alphaproteobacteria

Introduction

Biological nitrogen fixation (BNF) contributes substantially to the productivity of sustainable agriculture around the world and approximately 80% of biologically fixed nitrogen (N) is estimated to be contributed by the symbiotic association between root nodule bacteria (RNB) and leguminous plants [1]. This process of symbiotic nitrogen fixation (SNF) enables 175 million tons of atmospheric nitrogen (N2) to be fixed each year into a plant available form. SNF therefore reduces the need to apply fertilizer to provide bioavailable nitrogen, decreases greenhouse gas emissions derived from fertilizer manufacture, alleviates chemical leaching into the environment from the over application of fertilizer, and substantially enhances soil nitrogen for crop and animal production [24]. Because of substantial SNF benefits, considerable effort has been devoted to sourcing legumes from different geographical locations to improve legume productivity in different agricultural settings [3].

The Mediterranean legume Biserrula pelecinus L. is one of only three deep rooted annual legume species widely used in commerce with the potential to reduce the development of dryland salinity in Australia and was therefore introduced into Australia in 1994. Native RNB in Australian soil were not capable of nodulating B. pelecinus and therefore this host was inoculated with the inoculant strain Mesorhizobium ciceri bv. biserrulae WSM1271 [5] to obtain an effective symbiosis. Six years after the introduction of this legume into Western Australia, isolates were recovered from root nodules on B. pelecinus growing in Northam, Western Australia that were compromised in their nitrogen fixation capacity. The gradual replacement of the inoculant by established strains of RNB that are competitive for nodulation but suboptimal in N2 fixation threatens the successful establishment of this new legume in agriculture [6].

One of these poorly effective but competitive strains that was isolated from a nodule of B. pelecinus grown in the wheat belt of Western Australia can only fix <40% N2 compared to the original inoculant M. ciceri bv. biserrulae WSM1271. This strain has been designated as WSM2073T (= LMG 24608 = HAMBI 3006) and is now the recognized type strain for the species Mesorhizobium australicum [7]. The species name au.stra.li’cum. N.L. neut. adj. australicum is in reference to where this isolate originated from [7] and represents a dominant chromosomal type strain surviving as a soil saprophyte in the Western Australian wheat belt [6,8] that appears to have the capacity to acquire symbiotic genes through horizontal transfer [9].

In this report we present a summary classification and a set of general features for M. australicum strain WSM2073T together with the description of the complete genome sequence and its annotation. Here we reveal that a 455.7 Kb genomic island from the inoculant Mesorhizobium ciceri bv. biserrulae WSM1271 has been horizontally transferred into M. australicum strain WSM2073T and integrated into the phenylalanine-tRNA gene.

Classification and features

M. australicum strain WSM2073T is a motile, gram negative, non-spore-forming rod (Figure 1 Left and Center) in the order Rhizobiales of the class Alphaproteobacteria. They are moderately fast growing, forming 2–4 mm diameter colonies within 3–4 days and have a mean generation time of 4–6 h when grown in half Lupin Agar (½LA) broth [10] at 28 °C. Colonies on ½LA are white-opaque, slightly domed, moderately mucoid with smooth margins (Figure 1 Right). Strains of this organism are able to tolerate a pH range between 5.5 and 9.0. More information on the carbon source utilization and fatty acid profiles were described before [7]. Minimum Information about a Genome Sequence (MIGS) is given in Table 1.
Figure 1.

Images of M. australicum strain WSM2073T using scanning (Left) and transmission (Center) electron microscopy and the appearance of colony morphology on a solid medium (Right).

Table 1.

Classification and general features of M. australicum strain WSM2073T according to the MIGS recommendations [11].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [12]

 

Phylum Proteobacteria

TAS [13]

 

Class Alphaproteobacteria

TAS [14,15]

 

Order Rhizobiales

TAS [15,16]

 

Family Phyllobacteriaceae

TAS [15,17]

 

Genus Mesorhizobium

TAS [18]

 

Species Mesorhizobium australicum

TAS [7]

 

Gram stain

Negative

TAS [7]

 

Cell shape

Rod

TAS [7]

 

Motility

Motile

TAS [7]

 

Sporulation

Non-sporulating

TAS [19]

 

Temperature range

Mesophile

TAS [19]

 

Optimum temperature

28°C

TAS [7]

 

Salinity

Unknown

NAS

MIGS-22

Oxygen requirement

Aerobic

TAS [19]

 

Carbon source

Arabinose, gentibiose, glucose, mannitol & melibiose

TAS [7]

 

Energy source

Chemoorganotroph

TAS [19]

MIGS-6

Habitat

Soil, root nodule, host

TAS [7]

MIGS-15

Biotic relationship

Free living, Symbiotic

TAS [7]

MIGS-14

Pathogenicity

None

NAS [19]

 

Biosafety level

1

TAS [20]

 

Isolation

Root nodule of Biserrula pelecinus. L

TAS [7]

MIGS-4

Geographic location

Northam, Western Australia

TAS [6]

MIGS-5

Nodule collection date

August 2000

TAS [6]

MIGS-4.1

Longitude

116.947875

TAS [6]

MIGS-4.2

Latitude

-31.530408

TAS [6]

MIGS-4.3

Depth

10 cm

IDA

MIGS-4.4

Altitude

160 m

IDA

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 the Gene Ontology project [21]. If the evidence code is IDA, then the property was directly observed by one of the authors or an expert mentioned in the acknowledgements.

Figure 2 shows the phylogenetic neighborhood of M. australicum strain WSM2073T in a 16S rRNA sequence based tree. This strain clustered in a tight group which included M. shangrilense, M. loti and M. ciceri and had >99% sequence similarity with all four type strains. However, based on a polyphasic taxonomic study we have identified this strain to belong to a new species [7].
Figure 2.

Phylogenetic tree showing the relationships of M. australicum strain WSM2073T with some of the root nodule bacteria in the order Rhizobiales based on aligned sequences of the 16S rRNA gene (1,290 bp internal region). All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA [22]. The tree was built using the Maximum-Likelihood method with the General Time Reversible model. Bootstrap analysis [23] was performed to assess the support of the clusters. Type strains are indicated with a superscript T. Brackets after the strain name contain a DNA database accession number and/or a GOLD ID (beginning with the prefix G) for a sequencing project registered in GOLD [24] Published genomes are indicated with an asterisk.

Symbiotaxonomy

M. australicum strain WSM2073T has an extremely narrow legume host range for symbiosis only forming partially effective nitrogen-fixing root nodules on Biserrula pelecinus L [6]. This strain also nodulates the closely related species Astragalus membranaceus but does not nodulate 21 other legume species nodulated by Mesorhizobium spp. [6]. Strain WSM2073T has similar highly specific symbiotic nodulation capabilities to M. ciceri bv. biserrulae WSM1271, but is a poor N-fixer on B. pelecinus L.

Genome sequencing and annotation

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 US Department of Energy Joint Genome Institute (JGI) for projects of relevance to agency missions. The genome project is deposited in the Genomes OnLine Database [24] and the complete genome sequence 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 for Mesorhizobium australicum strain WSM2073T

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Illumina GAii shotgun library, 454 Titanium standard library and paired end 454 libraries

MIGS-29

Sequencing platforms

Illumina and 454 technologies

MIGS-31.2

Sequencing coverage

454 standard and paired end (28x) and Illumina (2159x); total 2187x

MIGS-30

Assemblers

Newbler v 2.3 and Velvet v 0.7.63, PHRAP SPS-4.24 and CONSED

MIGS-32

Gene calling method

Prodigal v.2.50, GenePrimp

 

Genbank ID

CP003358

 

Genbank Date of Release

December 28, 2012

 

GOLD ID

Gc02468

 

NCBI project ID

47287

 

Database: IMG

2509276022

 

Project relevance

Symbiotic nitrogen fixation, agriculture

Growth conditions and DNA isolation

M. australicum strain WSM2073T was grown to mid logarithmic phase in TY medium (a rich medium) [25] on a gyratory shaker at 28°C. DNA was isolated from 60 mL of cells using a CTAB (Cetyl trimethylammonium bromide) bacterial genomic DNA isolation method.

Genome sequencing and assembly

The draft genome of M. australicum strain WSM2073T was generated at the DOE Joint genome Institute (JGI) using a combination of Illumina [26] and 454 technologies [27]. For this, genome we constructed and sequenced an Illumina GAii shotgun library which generated 10,509,788 reads totaling 378.4 Mb, a 454 Titanium standard library which generated 235,807 reads and paired end 454 libraries with an average insert sizes of 26.3 Kb/10.9 Kb which generated 221,877/139,171 reads totaling 257.0 Mb of 454 data. All general aspects of library construction and sequencing performed in this project can be found at the DOE Joint Genome Institute website. The initial draft assembly contained 14 contigs in 1 scaffold. The 454 Titanium standard data and the 454 paired end data were assembled together with Newbler, version 2.3. The Newbler consensus sequences were computationally shredded into 2 Kb overlapping fake reads (shreds). Illumina sequencing data was assembled with VELVET, version 0.7.63 [28], 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 [2931] 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 [32], 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 59 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. The total size of the genome is 6,200,534 bp and the final assembly is based on 257 Mb of 454 draft data which provides an average 28× coverage of the genome and 13,385 Mb of Illumina draft data which provides an average 2159× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [33] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePrimp pipeline [34]. 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 [35], RNAMMer [36], Rfam [37], TMHMM [38], and SignalP [39]. Additional gene prediction analyses and functional annotation were performed within the Integrated Microbial Genomes (IMG-ER) platform [40].

Genome properties

The genome is 6,200,534 bp long with a 62.84% GC content (Table 3, Figure 3) and comprised of a single chromosome. From all the genes present in the genome, 6,013 were protein coding genes and 67 RNA only encoding genes. Two hundred and twenty one pseudogenes were also identified. The majority of protein coding genes (4,875; 80.18%) were assigned a putative function whilst the remaining protein coding genes were annotated as encoding hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

Graphical circular map of the chromosome of Mesorhizobium australicum WSM2073T. 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 Mesorhizobium australicum strain WSM2073T.

Attribute

Value

% of Total

Genome size (bp)

6,200,534

100

DNA coding region (bp)

5,371,783

86.63

DNA G+C content (bp)

3,896,642

62.84

Number of replicons

1

100

Extrachromosomal elements

0

 

Total genes

6,080

100

RNA genes

67

1.1

Protein-coding genes

6,013

98.9

Genes with function prediction

4,875

80.18

Genes assigned to COGs

4,877

80.21

Genes assigned Pfam domains

5,082

83.40

Genes with signal peptides

536

8.82

Genes with transmembrane helices

1,434

23.59

Table 4.

Number of protein coding genes of Mesorhizobium australicum WSM2073T associated with the general COG functional categories.

Code

Value

%age

Description

J

192

3.56

Translation, ribosomal structure and biogenesis

A

1

0.02

RNA processing and modification

K

450

8.34

Transcription

L

179

3.32

Replication, recombination and repair

B

5

0.09

Chromatin structure and dynamics

D

35

0.65

Cell cycle control, mitosis and meiosis

Y

0

0.00

Nuclear structure

V

60

1.11

Defense mechanisms

T

214

3.96

Signal transduction mechanisms

M

305

5.65

Cell wall/membrane biogenesis

N

42

0.78

Cell motility

Z

0

0.00

Cytoskeleton

W

1

0.02

Extracellular structures

U

115

2.13

Intracellular trafficking and secretion

O

180

3.33

Posttranslational modification, protein turnover, chaperones

C

302

5.59

Energy production conversion

G

511

9.47

Carbohydrate transport and metabolism

E

634

11.75

Amino acid transport metabolism

F

94

1.74

Nucleotide transport and metabolism

H

201

3.72

Coenzyme transport and metabolism

I

216

4.00

Lipid transport and metabolism

P

239

4.43

Inorganic ion transport and metabolism

Q

156

2.89

Secondary metabolite biosynthesis, transport and catabolism

R

699

12.95

General function prediction only

S

567

10.50

Function unknown

-

1203

19.79

Not in COGS

Total

5,748

-

-

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 Australian Research Council Discovery grant (DP0880896), 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)
Bioscience Division, Los Alamos National Laboratory
(3)
DOE Joint Genome Institute
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Department of Agriculture and Food

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