Open Access

Genome sequence of the clover symbiont Rhizobium leguminosarum bv. trifolii strain CC275e

  • Clément Delestre1,
  • Aurélie Laugraud2,
  • Hayley Ridgway3,
  • Clive Ronson4,
  • Maureen O’Callaghan2,
  • Brent Barrett5,
  • Ross Ballard6,
  • Andrew Griffiths5,
  • Sandra Young2,
  • Celine Blond3,
  • Emily Gerard2 and
  • Steve Wakelin2Email author
Standards in Genomic Sciences201510:121

DOI: 10.1186/s40793-015-0110-1

Received: 6 August 2015

Accepted: 2 November 2015

Published: 8 December 2015

Abstract

Rhizobium leguminosarum bv. trifolii strain CC275e is a highly effective, N2-fixing microsymbiont of white clover (Trifolium repens L.). The bacterium has been widely used in both Australia and New Zealand as a clover seed inoculant and, as such, has delivered the equivalent of millions of dollars of nitrogen into these pastoral systems. R. leguminosarum strain CC275e is a rod-shaped, motile, Gram-negative, non-spore forming bacterium. The genome was sequenced on an Illumina MiSeq instrument using a 2 × 150 bp paired end library and assembled into 29 scaffolds. The genome size is 7,077,367 nucleotides, with a GC content of 60.9 %. The final, high-quality draft genome contains 6693 protein coding genes, close to 85 % of which were assigned to COG categories. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JRXL00000000. The sequencing of this genome will enable identification of genetic traits associated with host compatibility and high N2 fixation characteristics in Rhizobium leguminosarum. The sequence will also be useful for development of strain-specific markers to assess factors associated with environmental fitness, competiveness for host nodule occupancy, and survival on legume seeds (New Zealand Ministry of Business, Innovation and Employment program, ‘Improving forage legume-rhizobia performance’ contract C10X1308 and DairyNZ Ltd.).

Keywords

Root-nodule bacteria Microsymbiont Nitrogen fixation Rhizobia Alphaproteobacteria

Introduction

White clover ( Trifolium repens ) is the most widely established and important legume in pastures in New Zealand [1] and globally [2]. In symbiosis with nodule-forming Rhizobium leguminosarum bacteria of the biovar trifolii (hereafter R. leguminosarum bv trifolii), clover plants fix atmospheric nitrogen into a plant-available, thus providing an economically and environmentally sustainable method of maintaining soil fertility and pasture production. Across New Zealand there are 11,400+ farms using pastures containing forage legumes (mostly white clover), covering 7.88 million hectares [3]. This constitutes about 29 % of the total land area and excludes hill country/tussock grasslands. Estimates of nitrogen input from legumes vary, however average at 185 kg N ha−1 yr−1 for pastures with a slope less than 12° [4]. Based on recent average costs of urea fertilizer (2013–14 average), the value of N2 fixation into New Zealand pastures is 1.8 billion per year; this is highly conservative as it does not encompass the value of increased forage quality, N2 fixation in extensive hill country systems, and reduced environmental costs.

R. leguminosarum bv trifolii strains vary extensively in their ability to form nodules with white clover [5], and also their effectiveness at fixing nitrogen during symbiosis [6]. As such, dedicated selection and screening programs have played a vital role in ensuring clover (and, of course, other legume species) are matched with an optimal rhizobia symbiont [7]. These are most commonly delivered into farming systems as rhizobia-inoculated seed [8].

The inoculation of white clover seed with rhizobia commenced in New Zealand in the early 20th century [8]. In addition to New Zealand produced inoculant strains, R. leguminosarum bv trifolii strain CC275e was sourced from Australia [9]. From 1974, the inoculant production in New Zealand industry was phased-out and the sole commercial strain for inoculation of white clover seed was strain CC275e, which was then replaced with R. leguminosarum bv trifolii strain TA1 (also from Australia) around 2005. Thus, R. leguminosarum bv trifolii strain CC275e was in widespread use in New Zealand for approximately three decades, and is likely to have contributed billions of dollars of nitrogen into New Zealand’s pastoral systems. On white clover, R. leguminosarum bv trifolii strain CC275e has been reported to fix more nitrogen than strain TA1 and has greater persistence in soils [9]. The decision by the inoculant industry to replace strain CC275e with strain TA1 was based on ease of production.

A number of synonyms of strain R. leguminosarum bv trifolii strain CC275e exist. In New Zealand, a culture of strain CC275e was received by the Plant Diseases Division of the Department of Scientific and Industrial Research in 1974 and a re-isolate of this culture is referred to as strain PDD2163. Furthermore, in New Zealand, strain CC275e has also been referred to as strain W16 [10], but when used commercially was most commonly known as strain NZP561 [11]. In Australia, where the bacterium originates, early work referred to it as strain W16 or Strain Hastings T71 [10]. However, strain CC275e was the designation used when the bacterium was deposited in the CSIRO (Canberra) culture collection [12], and this is the most commonly used synonym. In the American Type Culture Collection, the bacterium is referred to as ATCC 35181. For this study, an original R. leguminosarum bv trifolii strain CC275e culture was obtained from the Australian Inoculant Research Group (Gosford, NSW, Australia). These sequence data complements those of Trifolium -nodulating R. leguminosarum bv trifolii strain WSM1325 (GenBank ID 241202755), strain WSM2304 (GenBank ID 209547612), strain WSM1689 (GenBank ID 752843554), and strain TA1 (GenBank ID 653806106).

Organism information

Classification and features

Rhizobium leguminosarum bv. trifolii strain CC275e is a Gram-negative, motile, non-spore forming, non-encapsulated, rod shaped bacterium (Fig. 1). Colonies of R. leguminosarum bv trifolii strain CC275e form within 4 to 5 days when grown on yeast mannitol agar (YMA; [13]) at 25 °C. Colonies are white-opaque, domed and glassy in appearance, with smooth margins.
Fig. 1

TEM micrograph of three Rhizobium leguminosarum bv. trifolii CC275e cells. The length of the bar = 1 um

Rhizobium leguminosarum and closely related species are generally regarded as non-fastidious, chemo-organotrophic bacteria [14]. Although the wider substrate requirements for strain CC275e have not been formally described, the authors support this classification based on personal experience in the handling, cultivation and fermentation of R. leguminosarum bv trifolii strain CC275e.

The R. leguminosarum bv trifolii strain CC275e genome contains three (100 % identical) copies of the 16S rRNA gene. Alignment of these nucleotide sequences against other species supports close 16S rRNA phylogeny with R. leguminosarum originating from other legume hosts (Fig. 2). The 16S rRNA gene sequence has highest similarity to other accessions of R. leguminosarum biovars trifolii (99.8 %) and phaseoli (99.6 %) (Fig. 2) - the GenBank accession numbers for these are provided in Additional file 1: Table S1. The species is placed within the order Rhizobiales of the class Alphaproteobacteria [15]. Minimum information about the Genome Sequence (MIGS) is provided in Table 1.
Fig. 2

Phylogenetic tree showing relationship of R. leguminosarum bv trifolii CC275e with closely and distantly related taxa in the order Rhizobiales. The tree is based on 1498 bp length alignment of the 16S rRNA gene using MUSCLE with default parameters [31]. The tree was constructed using maximum likelihood method, with the General Time Reversible model (rate 4 classes; [32]). Nodes with bootstrap (1000 repetitions) support > 50 % are shown [33]. Accession numbers relating to the nucleotide sequences for each of the strains are listed in Additional file 1: Table S1

Table 1

Classification and general features of Rhizobium leguminosarum bv. trifolii strain CC275e according to the MIGS recommendations [34]

MIGS ID

Property

Term

Evidence codesa

 

Current classification

Domain Bacteria

TAS [35]

  

Phylum Proteobacteria

TAS [36]

  

Class Alphaproteobacteria

TAS [37]

  

Order Rhizobiales

TAS [38]

  

Family Rhizobiaceae

TAS [15]

  

Genus Rhizobium

TAS [15]

  

Species Rhizobium leguminosarum

TAS [14]

  

Strain CC275e

TAS [12]

 

Gram Stain

Negative

TAS [15]

 

Cell Shape

Rod

TAS [15]

 

Motility

Motile

TAS [15]

 

Sporulation

Non spore-forming

TAS [15]

 

Temperature range

Mesophile

TAS [15]

 

Optimum temperature

28 °C

NAS

 

pH range; optimum

Unknown

NAS

 

Carbon source

Varied, chemoorganotrophic

TAS [15]

MIGS-6

Habitat

Soil, root nodule

TAS [12]

MIGS–6.3

Salinity

Non–halophile

NAS

MIGS–22

Oxygen requirement

Aerobic

TAS [15]

MIGS–15

Biotic relationship

Free living, legume symbiotic

TAS [15]

MIGS–14

Pathogenicity

Non–pathogen

TAS [15, 39]

MIGS–4

Geographic location

Tasmania, Australia

TAS [12]

MIGS–5

Sample collection date

1966

TAS [12]

MIGS–4.1

Latitude

Not recorded

 

MIGS–4.2

Longitude

Not recorded

 

MIGS–4.3

Depth

Not recorded

 

MIGS–4.4

Altitude

Not recorded

 

aEvidence codes – IDA Inferred from Direct Assay, 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 [34]

Symbiotaxonomy

R. leguminosarum bv trifolii strain CC275e is nodule forming (Nod+) and N2 fixing (Fix+) on a range of annual and perennial clover host species. The original isolation of R. leguminosarum bv trifolii strain CC275e was from Trifolium repens L. collected from Montague, North Western Tasmania [12], and has been used commercially due to its efficacy at forming symbioses and fixation of nitrogen on white clover hosts [9]. The strain is also moderately effective (sensu Brockwell et al. [12]) on T. fragiferum L. (strawberry clover; perennial), and T. michelianum Savi, (balansa clover; annual). On T. subterraneum L. (subterranean clover; annual), T. purpureum Lois. (purple clover; annual), and T. hirtum All. (rose clover; annual), strain CC275e has been described as effective [12].

Genome sequencing information

Genome project history

R. leguminosarum bv trifolii strain CC275e was selected for sequencing based on its long history of commercial use as an inoculant for various clover (Trifolium spp.) hosts in Australia and New Zealand. In symbiosis with clover, this strain of bacteria has provided biologically-fixed nitrogen into soils for several decades, and thereby contributed to the fertility and productivity of pastoral agricultural systems in two countries. As part of a New Zealand MBIE-funded program, ‘Improving forage legume-rhizobia performance’ (C10X1308), the genomics of elite host nodulating (nod+) and N2 fixing (fix+) strains are being compared with closely related, ineffective strains. The aim is to identify markers to facilitate rhizobia selection programs, and to provide experimental tools for host colonization/competition experiments. Based on efforts in other R. leguminosarum bv trifolii strains (see accessions listed in the introduction) a sequencing strategy was developed using a predicted genome size of approximately 7 Mb. The genome sequencing and assembly was completed in 2014; summary information on the project is given in Table 2. The final R. leguminosarum bv trifolii CC275e genome assembly is a high-quality draft on 29 scaffolds, and resulted from approximately 150× sequencing coverage.
Table 2

Genome sequencing project information for Rhizobium leguminosarum bv. trifolii strain CC275e

MIGS ID

Property

Term

MIGS-31

Finishing quality

High-quality draft

MIGS-28

Libraries Used

Illumina TruSeq™ DNA Sample Preparation Kit V2, 2 × 150 bp paired end library

MIGS-29

Sequencing platform

Illumina MiSeq™

MIGS-31.2

Fold coverage

3.75 million reads, ≈150 × genome coverage

MIGS-30

Assemblers

A5, SSPACE, Velvet Optimiser

MIGS-32

Gene calling method

Glimmer 3

 

Locus Tag

 
 

Genbank ID

JRXL00000000

 

Genbank Date of Release

27st October, 2014

 

GOLD ID

Gp0113226

 

BIOPROJECT

259682

MIGS-13

Source Material Identifier

ATCC 35181

 

Project relevance

Symbiotic N2 fixation, agriculture

Growth conditions and genomic DNA preparation

A loop of a single colony of R. leguminosarum bv trifolii CC275e was inoculated into YM broth [13] and grown to mid-log phase via incubation at 28 °C at 200 rpm for 12 h. DNA was extracted from the cell culture using a Gentra Puregene Cell kit (Qiagen). Spectrophotometry was used to quantify the DNA and ensure quality was sufficient for sequencing analysis (Nanodrop Thermo Scientific).

Genome sequencing and assembly

Genome sequencing was conducted through NZGL (contract NZGL00940) at Massey University (MGS). Sequencing was performed on an Illumina MiSeqTM instrument (details in Table 2), using 2 × 150 bp paired-end (PE) library with an average insert size of 420 bp. The sequencing run generated 3,751,285 reads totaling 1088 Mb of data.

Reads were assembled using the Java Assembling and Scaffolding Tool (JAST; [16]). Quality control of the sequence reads was conducted in Flexbar [17], and initial de novo assembly in A5 [18]; this resulted in 52 contigs. Bowtie2 [19] and Velvet [20] were further used to optimize the assembly, using the genome of the closely strain R. leguminosarum strain WSM1325 (Fig. 2) as a reference (NCBI accession 241202755). SSPACE [21] was used to assemble the 35 contigs into 29 scaffolds (Table 3). Summary details of the sequencing process are given in Table 2.
Table 3

Genome statistics for Rhizobium leguminosarum bv. trifolii strain CC275e

Attribute

Value

% of total

Genome size (bp)

7,077,367

100.00

DNA coding (bp)

6,201,447

87.62

DNA G + C (bp)

4,306,744

60.90

DNA scaffolds

29

 

Total genes

6747

100.00

Protein coding genes

6693

99.00

RNA genes

54

0.80

Pseudo genes

not determined

not determined

Genes in internal clusters

not determined

not determined

Genes with function prediction

5018

74.37

Genes assigned to COGs

5722

84.80

Genes with Pfam domains

5682

84.22

Genes with signal peptides

531

7.87

Genes with transmembrane helices

1584

23.48

CRISPR repeats

0

 

Genome annotation

Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). Clusters of orthologous groups of proteins (COGs) were predicted using COGnitor [22], and the presence of signal peptides was detected using SignalP [23]. Pfam domains were predicted using HMMER [24] against the Pfam-A database [25]. Transmembrane predictions and CRISPR repeats were found in Genious [26] using the Transmembrane prediction (http://www.geneious.com/plugins/transmembrane-prediction-plugin) and CRT plugins [27] respectively.

Genome properties

The genome of R. leguminosarum bv trifolii strain CC275e is estimated to be 7,077,367 nucleotides in size (Table 3). The GC content is 60.9 % which is similar to closely related strains such as R. leguminosarum bv trifolii strain TA1 (60.74 %; [28]). The final draft consists of 29 scaffolds, the largest of which is 1,609,666 bp and the smallest 1167 bp. In total, 6747 genes were identified, 99 % of these were protein coding and the rest rRNA genes (Table 3). The majority of protein coding genes (84.22 %) have functionality predicted against COG categories; these are listed in Table 4. The remainder are listed as hypothetical.
Table 4

Number of protein coding genes of Rhizobium leguminosarum bv. trifolii strain CC275e associated with the general COG functional categories

Code

Value

% of total

COG category

J

189

2.69

Translation

A

0

0.00

RNA processing and modification

K

624

8.88

Transcription

L

186

2.65

Replication

B

2

0.03

Chromatin structure and dynamics

D

38

0.54

Cell cycle control

Y

0

0.00

Nuclear structure

V

64

0.91

Defense mechanisms

T

361

5.14

Signal transduction mechanisms

M

297

4.23

Cell wall/membrane/ biogenesis

N

96

1.37

Cell motility

Z

0

0.00

Cytoskeleton

W

0

0.00

Extracellular structures

U

74

1.05

Intracellular trafficking

O

185

2.63

Posttranslational modification

C

295

4.20

Energy production and conversion

G

646

9.19

Carbohydrate transport and metabolism

E

672

9.56

Amino acid transport and metabolism

F

108

1.54

Nucleotide transport and metabolism

H

151

2.15

Coenzyme transport and metabolism

I

238

3.39

Lipid transport and metabolism

P

234

3.33

Inorganic ion transport and metabolism

Q

95

1.35

Secondary metabolites biosynthesis

R

623

8.87

General function prediction only

S

544

7.74

Function unknown

-

1305

18.57

Not in COGs

Analysis of the genome by Eckhart gel electrophoresis [29] (Fig. 3) revealed the presence of six mega-plasmids. Mega-plasmids are typical of the ‘ancillary genome’ present in many R. leguminosarum strains [30] and commonly host many of the recognition factors associated with host compatibility, and nitrogen fixation. Based on the known mega-plasmid profile of R. leguminosarum bv trifolii strain WSM1325 (Fig. 3), the mega-plasmids in R. leguminosarum bv trifolii strain CC275e are approximately >1000, 500, 280, 280, 150, and 140 kb in size. As yet it is unknown to which scaffolds these mega-plasmids are associated.
Fig. 3

Eckhardt gel electropherogram showing ‘mega-plasmid’ profiles of R. leguminosarum bv trifolii strain CC275e against strains TA1 and WSM1325. The bright central band for strain CC275e represents co-migration of two similarly sized plasmids. Also, note double band at bottom of strain CC275e lane profile. The size of plasmids in reference strain WSM1325 are 294, 350, 516, and 829, 661, 516, 350, and 294 kb

Conclusions

Rhizobium leguminosarium bv. trifolii bacteria are an important resource for agricultural production [1, 2, 4]. In symbiosis with a suitable legume host (legume root nodules), atmospheric nitrogen fixed by these bacteria provides a source of plant nutrition that increases the farming system fertility in an economically and environmentally sustainable manner. Strains of R. leguminosarum bv trifolii vary in host-compatibility between legume species [5], and their nitrogen fixation efficacy when in symbiosis [6]. Understanding the genetic factors controlling these, and other phenotypes such as saprophytic survival, and desiccation tolerance, will enable increased utilization of R. leguminosarum bv trifolii for farming systems. The strain R. leguminosarum bv trifolii strain CC275e has been commercially used as an inoculant for white-clover for several decades [9]. The genome sequencing of this ‘highly efficacious’ bacterium, allows for the identification of genetic factors associated with desirable phenotypes (see previous). This will be achieved by comparison of the R. leguminosarum bv trifolii strain CC275e with closely related stains (e.g. based on 16S rRNA similarity) that differ in one or more phenotypes.

Abbreviations

CSIRO: 

Commonwealth scientific and industrial research organisation

Fix+

Nitrogen fixation positive

NZGL: 

New Zealand genomics Ltd

Nod+

Nodulation positive

MGS: 

Massey genome service

MBIE: 

Ministry of business, innovation and employment

R. leguminosarum bv trifolii

Rhizobium leguminosarum symbiovar trifolii

TEM: 

Transmission electron microscopy

YM: 

Yeast mannitol

Declarations

Acknowledgements

This work was funded through the New Zealand MBIE and DairyNZ funded programme “Improving forage legume-rhizobia performance” (C10X1308). Clément Delestre acknowledges the AgResearch bioinformatics team for internship funding. Sequencing was performed by MGS, and was coordinated by Lorraine Berry under NZGL contract NZGL00940 within the public-good funding stream. Sample QC, library QC, and library preparation was performed by Xiaoxiao Lin, sequencing by Richard Fong, and data QC by Mauro Truglio. Prof. Michael Hynes (University of Calgary) provided useful knowledge on R. leguminosarum mega-plasmids. TEM was conducted by Dr Duane Harland and James Vernon (AgResearch).

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)
University of Bordeaux, IT Science
(2)
AgResearch Ltd, Lincoln Campus
(3)
Faculty of Agriculture and Life Sciences, Lincoln University
(4)
Department of Microbiology and Immunology, University of Otago
(5)
AgResearch Ltd, Grasslands Research Centre
(6)
South Australian Research and Development Institute

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