Open Access

High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York

  • Rui Tian1,
  • Matthew Parker2,
  • Rekha Seshadri3,
  • TBK Reddy3,
  • Victor Markowitz4,
  • Natalia Ivanova3,
  • Amrita Pati3,
  • Tanja Woyke3,
  • Mohammed N Baeshen6, 7,
  • Nabih A Baeshen5, 6,
  • Nikos Kyrpides3, 5 and
  • Wayne Reeve1Email author
Standards in Genomic Sciences201510:24

https://doi.org/10.1186/s40793-015-0008-y

Received: 13 February 2015

Accepted: 16 April 2015

Published: 16 May 2015

Abstract

Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft genome sequence information and annotation. The 10,118,060 high-quality draft genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding genes and 108 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Keywords

Root-nodule bacteriaNitrogen fixationSymbiosis Alphaproteobacteria GEBA-RNB

Introduction

Strain Th.b2 is a representative of a widely distributed Bradyrhizobium lineage used by several common legumes indigenous to forested habitats in eastern North America. Strain Th.b2 was sampled in 1991 from a population of the annual legume Amphicarpaea bracteata in Johnson City, NY. Surveys of other A. bracteata populations in the eastern United States based on 20 isozyme markers found that strains similar or identical to Th.b2 were present in 19 of 24 sites across six states (IL, IN, WI, MI, NY, PA [1]). Based on both isozyme data and rRNA sequencing, isolates that were similar or identical to Th.b2 were also detected in nodule samples from two common herbaceous perennial legumes, Apios americana and Hylodesmum glutinosum , that often occur in woodland habitats together with Amphicarpaea bracteata [2]. A multilocus sequence analysis found strains in North Carolina populations of A. bracteata that were similar or identical to Th.b2 [3], and also detected a highly similar strain on another herbaceous perennial legume, Desmodium paniculatum , that is widely distributed across eastern North America [4].

Based on these field surveys, the Bradyrhizobium lineage represented by strain Th.b2 appears to be relatively host-specific to legumes in these four genera ( Amphicarpaea , Apios , Desmodium , Hylodesmum), because widespread sampling of sympatric legumes in eleven other genera have not detected this group [3,5,6]. However, inoculation experiments are needed to understand whether the Th.b2 lineage lacks the ability to nodulate these other genera, or alternatively, may simply be a poor competitor for nodulation in the presence of other bacterial strains that are their preferred symbionts.

It should also be noted that the eastern North American symbionts of Amphicarpaea , Apios , Desmodium and Hylodesmum are not phylogenetically homogeneous at housekeeping loci. Horizontal transfer of the symbiosis island (SI) region of the Bradyrhizobium chromosome [7] from a member of the Th.b2 clade to a distantly related Bradyrhizobum lineage has apparently enabled the recipient to gain the ability to interact with some of the normal legume hosts of the Th.b2 clade [3].

Bacteria that are closely related to Th.b2 have also been found in Japan associated with an Asian species of Amphicarpaea (A. edgeworthii) [6]. Surprisingly, strain Th.b2 lacks the ability to form nodules on A. edgeworthii, although Japanese strains from A. edgeworthii are effective nitrogen-fixing symbionts for the American legume A. bracteata [8,9]. These differences appear to be related to variation between related East Asian and North American strains in the synthesis of rhizobitoxine [8].

Here we provide an analysis of the high-quality permanent draft genome sequence of Bradyrhizobum sp. Th.b2, one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal [10], whose properties may provide useful insights about the evolution of symbiotic specificity and its relationship to SI region horizontal transfer in Bradyrhizobium .

Organism information

Classification and features

Bradyrhizobium sp. Th.b2 is a motile, non-sporulating, non-encapsulated, Gram-negative strain in the order Rhizobiales of the class Alphaproteobacteria . The rod shaped form has dimensions of approximately 0.5 μm in width and 1.5-2.0 μm in length (Figure 1 Left and Center). It is relatively slow growing, forming colonies after 6–7 days when grown on half strength Lupin Agar (½LA) [11], tryptone-yeast extract agar (TY) [12] or a modified yeast-mannitol agar (YMA) [13] at 28°C. Colonies on ½LA are opaque, slightly domed and moderately mucoid with smooth margins (Figure 1 Right).
Figure 1

Images of Bradyrhizobium sp. Th.b2 using scanning (Left) and transmission (Center) electron microscopy as well as light microscopy to visualize colony morphology on solid media (Right).

Figure 2 shows the phylogenetic relationship of Bradyrhizobium sp. Th.b2 in a 16S rRNA gene sequence based tree. This strain is phylogenetically most closely related to the type strains Bradyrhizobium icense LMTR 13T and Bradyrhizobium paxllaeri LMTR 21T, with a 16S rRNA gene sequence identity of 99.77% to the corresponding gene sequence of each type strain based on alignment using the EzTaxon-e server [14,15].
Figure 2

Phylogenetic tree highlighting the position of Bradyrhizobium sp. Th.b2 (shown in blue print) relative to other type and non-type strains in the Bradyrhizobium genus using a 1,310 bp intragenic sequence of the 16S rRNA gene. Azorhizobium caulinodans ORS 571T sequence was used as an outgroup. All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA, version 5.05 [21]. The tree was built using the maximum likelihood method with the General Time Reversible model. Bootstrap analysis 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 [16] have the GOLD ID mentioned after the strain number and are represented in bold, otherwise the NCBI accession number is provided.

Minimum Information about the Genome Sequence (MIGS) is provided in Table 1 and Additional file 1: Table S1.
Table 1

Classification and general features of Bradyrhizobium sp. Th.b2 in accordance with the MIGS recommendations [27] published by the Genome Standards Consortium [28]

MIGS ID

Property

Term

Evidence code

 

Classification

Domain Bacteria

TAS [29]

  

Phylum Proteobacteria

TAS [30,31]

  

Class Alphaproteobacteria

TAS [31,32]

  

Order Rhizobiales

TAS [33]

  

Family Bradyrhizobiaceae

TAS [34]

  

Genus Bradyrhizobium

TAS [35]

  

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

 

pH range; Optimum

Unknown

NAS

 

Carbon source

Varied

NAS

 

Energy source

Chemoorganotroph

NAS

MIGS-6

Habitat

Soil, root nodule, host

TAS [1]

MIGS-6.3

Salinity

Non-halophile

NAS

MIGS-22

Oxygen requirement

Aerobic

NAS

MIGS-15

Biotic relationship

Free living, symbiotic

TAS [1]

MIGS-14

Pathogenicity

Non-pathogenic

NAS

 

Biosafety level

1

TAS [36]

 

Isolation

Root nodule of Amphicarpaea bracteata

TAS [1]

MIGS-4

Geographic location

Johnson City, New York

TAS [1]

MIGS-5

Sample collection date

1991

IDA

MIGS-4.1

Latitude

42.107

IDA

MIGS-4.2

Longitude

−75.9691

IDA

MIGS-4.3

Depth

5 cm

IDA

MIGS-4.4

Altitude

255 m

IDA

Evidence 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). Evidence codes are from the Gene Ontology project [37,38].

Symbiotaxonomy

Strain Th.b2 was isolated in 1991 from a population of the annual legume Amphicarpaea bracteata in Johnson City, NY. Isolates that were similar or identical to Th.b2 were also detected in nodule samples from two common herbaceous perennial legumes, Apios americana and Hylodesmum glutinosum , that often occur in woodland habitats together with Amphicarpaea bracteata [2]. Th.b2 lacks the ability to form nodules on the Asian species Amphicarpaea. edgeworthii, which is associated with a strain closely related to Th.b2 from Japan [6,8].

Genome sequencing 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 Genomic Encyclopedia of Bacteria and Archaea, Root Nodulating Bacteria (GEBA-RNB) project at the U.S. Department of Energy, Joint Genome Institute (JGI). The genome project is deposited in the Genomes OnLine Database [16] and a high-quality permanent draft genome sequence in IMG [17]. Sequencing, finishing and annotation were performed by the JGI using state of the art sequencing technology [18]. A summary of the project information is shown in Table 2.
Table 2

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

High-quality permanent draft

MIGS-28

Libraries used

Illumina Standard PE

MIGS-29

Sequencing platforms

Illumina HiSeq2000

MIGS-31.2

Fold coverage

Illumina, 120.4x

MIGS-30

Assemblers

Velvet version 1.1.04; Allpaths-LG version r42328

MIGS-32

Gene calling method

Prodigal 1.4

 

Locus Tag

K359

 

GenBank ID

AUGA00000000

 

GenBank Date of Release

June 13, 2014

 

GOLD ID

Gp0014287 [46]

 

BIOPROJECT

195826

MIGS-13

Source Material Identifier

Th.b2

 

Project relevance

Symbiotic N2 fixation, agriculture

Growth conditions and genomic DNA preparation

Bradyrhizobium sp. Th.b2 was cultured to mid logarithmic phase in 60 ml of TY rich media on a gyratory shaker at 28°C [19]. DNA was isolated from the cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method [20].

Genome sequencing and assembly

The draft genome of Bradyrhizobium sp. th.b2 was generated at the DOE Joint Genome Institute (JGI) using the Illumina technology [22]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 20,348,156 reads totaling 3,052.2 Mbp. All general aspects of library construction and sequencing were performed at the JGI and details can be found on the JGI website [23]. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts (Mingkun L, Copeland A, Han J, Unpublished). Following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet (version 1.1.04) [24], (2) 1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim [25], (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG (version r42328) [26]. 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 274 contigs in 266 scaffolds. The total size of the genome is 10.1 Mbp and the final assembly is based on 1,216.8 Mbp of Illumina data, which provides an average 120.4x coverage of the genome.

Genome annotation

Genes were identified using Prodigal [39], as part of the DOE-JGI genome annotation pipeline [40,41] 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 [42] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [43]. 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 [44]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes-Expert Review (IMG-ER) system [45] developed by the Joint Genome Institute, Walnut Creek, CA, USA.

Genome properties

The genome is 10,118,060 nucleotides with 63.25% GC content (Table 3) and comprised of 266 scaffolds. From a total of 9,919 genes, 9,809 were protein encoding and 108 RNA only encoding genes. The majority of genes (70.75%) 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.
Table 3

Genome statistics for Bradyrhizobium sp. Th.b2

Attribute

Value

% of Total

Genome size (bp)

10,118,060

100.00

DNA coding (bp)

8,412,367

83.14

DNA G + C (bp)

6,399,174

63.25

DNA scaffolds

266

100

Total genes

9,917

100.00

Protein coding genes

9,809

98.91

RNA genes

108

1.09

Pseudo genes

0

0.00

Genes in internal clusters

713

7.19

Genes with function prediction

7,016

70.75

Genes assigned to COGs

5,576

56.23

Genes with Pfam domains

71.85

72.45

Genes with signal peptides

978

9.86

Genes coding transmembrane helices

2,166

21.84

CRISPR repeats

0

0.00

Table 4

Number of genes associated with the general COG functional categories

Code

Value

% of total (6,228)

COG category

J

199

3.20

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

520

8.35

Transcription

L

197

3.16

Replication, recombination and repair

B

3

0.05

Chromatin structure and dynamics

D

30

0.48

Cell cycle control, cell division, chromosome partitioning

V

103

1.65

Defense mechanisms

T

248

3.98

Signal transduction mechanisms

M

290

4.66

Cell wall/membrane/envelope biogenesis

N

72

1.16

Cell motility

U

118

1.89

Intracellular trafficking, secretion, and vesicular transport

O

200

3.21

Posttranslational modification, protein turnover, chaperones

C

432

6.94

Energy production and conversion

G

382

6.13

Carbohydrate transport and metabolism

E

702

11.27

Amino acid transport and metabolism

F

81

1.30

Nucleotide transport and metabolism

H

208

3.34

Coenzyme transport and metabolism

I

391

6.28

Lipid transport and metabolism

P

338

5.43

Inorganic ion transport and metabolism

Q

301

4.83

Secondary metabolite biosynthesis, transport and catabolism

R

799

12.83

General function prediction only

S

614

9.86

Function unknown

-

4,341

43.77

Not in COGS

Conclusions

Bradyrhizobium sp. Th.b2 was isolated from a root nodule of Amphicarpaea bracteata collected from Johnson City, New York. Little is currently known of the symbiotic associations of its host Amphicarpaea bracteata . This strain belongs to a member of a widely distributed Bradyrhizobium lineage, isolated from diverse legume hosts in North, Central and South America and South Africa. Phylogenetically, Th.b2 is separated from the most closely related species Bradyrhizobium icense LMTR 13T and Bradyrhizobium paxllaeri LMTR 21T, both isolated from root nodules of Phaseolus lunatus (Lima bean) in Peru [47]. Th.b2 may therefore be a novel species of Bradyrhizobium . A total of 25 Bradyrhizobium genomes have now been sequenced as part of the GEBA-RNB project [10]. Of these 25 strains, Th.b2 has the second largest genome size (10.1 Mbp), gene count (9,917) and COG % and the lowest coding base count % (83.17). The genome attributes of Bradyrhizobium sp. Th.b2, in conjunction with other Bradyrhizobium genomes from GEBA-RNB project, will be important for the understanding of the biogeography of Bradyrhizobium spp. interactions required for the successful establishment of effective symbioses with their diverse hosts.

Abbreviations

GEBA-RNB: 

Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria

JGI: 

Joint Genome Institute

½LA: 

half strength Lupin Agar

TY: 

Tryptone Yeast

YMA: 

Yeast Mannitol Agar

CTAB: 

Cetyl Trimethyl Ammonium Bromide

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. We thank Gordon Thompson (Murdoch University) for the preparation of SEM and TEM photos. We would also like to thank the Center of Nanotechnology at King Abdulaziz University for their support.

Authors’ Affiliations

(1)
Centre for Rhizobium Studies, Murdoch University
(2)
Binghamton University, State University of New York
(3)
DOE Joint Genome Institute
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Department of Biological Sciences, Faculty of Science, King Abdulaziz University
(6)
Center of Nanotechnology, King Abdulaziz University
(7)
Department of Biological Sciences, Faculty of Science, Jeddah University

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