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High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556T
Standards in Genomic Sciences volume 10, Article number: 64 (2015)
Burkholderia dilworthii strain WSM3556T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. WSM3556T thus represents a potential inoculant quality strain for L. ambigua for which we describe the general features, together with genome sequence and annotation. The 7,679,067 bp high-quality permanent draft genome is arranged in 140 scaffolds of 141 contigs, contains 7,059 protein-coding genes and 64 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.
Over the last decade, agricultural scientists have sought to discover perennial legumes from a wide range of natural environments to develop new plants for grazing systems . It is thought that these plants might be more resilient to changing rainfall patterns, such as in the target environments of Western Australia. Here, winter rainfall has declined by 20 % in the last two decades , although more frequent summer rainfall events have been experienced. In the fynbos biome of South Africa, several species that offer potential for domestication have been discovered [1, 3]. These legumes are frequently nodulated by Burkholderia bacteria in the class Betaproteobacteria [3, 4]. The symbiosis between these Burkholderia and legumes from the genera Lebeckia and Rhynchosia fix atmospheric nitrogen to enable their cultivation on infertile soils [4–7]. Lebeckia ambigua is proving well adapted to Western Australia  because in areas where it is naturally found in South Africa the soil and climatic conditions approximate those of Western Australia.
Nodules and seeds of L. ambigua were collected in four expeditions to the Western Cape of South Africa between 2002 and 2007. The isolation of bacteria from these nodules gave rise to a collection of 23 strains that were identified as Burkholderia . Unlike most of the previously studied nodulating Burkholderia strains, this South African group appears to associate with papilionoid forage legumes, rather than Mimosa species. WSM3556T belongs to a subgroup of strains that were isolated in 2004 from nodules collected south west of Darling, in a natural rangeland site on the southern border of the Grotto Bay Nature Reserve . The soil at the site of collection was deep sand with a pH of 6. Burkholderia dilworthii strain WSM3556T was isolated from those nodules and is effective at fixing nitrogen with L. ambigua and L. sepiaria. The nodules formed by these symbioses are crotaloid and indeterminate .
WSM3556T thus represents a potential inoculant quality strain for L. ambigua, which is being developed as a grazing legume adapted to infertile soils that receive 250–400 mm annual rainfall in southern Australia and is therefore of special interest to the RNB chapter of the GEBA project. Here we present a summary classification and a set of general features for Burkholderia dilworthii strain WSM3556T together with the description of the permanent draft genome sequence and annotation.
Classification and features
Burkholderia dilworthii strain WSM3556T is a motile, Gram-negative, non-spore-forming rod (Fig. 1 Left, Center) in the order Burkholderiales of the class Betaproteobacteria . The rod-shaped form varies in size with dimensions of 0.9–2 μm in width and 0.4–3.0 μm in length (Fig. 1 Left). It is fast growing, forming 0.4–2 mm diameter colonies after 24 h when grown on half Lupin Agar  and TY  at 28 °C. Colonies on ½LA are white-opaque, slightly domed, moderately mucoid with smooth margins (Fig. 1 Right). Additional physiological properties of this strain were previously published .
Figure 2 shows the phylogenetic relationship of Burkholderia dilworthii strain WSM3556T in a 16S rRNA gene sequence based tree. This strain is most similar to Burkholderia rhynchosiae WSM3937T and Burkholderia phytofirmans PsJNT based on the 16S rRNA with sequence identities of 98.50 % and 98.11 %, respectively, as determined using the EzTaxon-e server . Burkholderia rhynchosiae WSM3937T has been isolated from Rhynchosia ferulifolia , a herbaceous legume from the fynbos biome in South Africa . Burkholderia phytofirmans PsJNT was isolated from surface sterilized onion roots and has plant growth promoting properties on various plants, however it has not been reported in association with legumes . Minimum Information about the Genome Sequence of WSM3556T is provided in Table 1.
Burkholderia dilworthii strain WSM3556T belongs to a group of Burkholderia strains that nodulate papilionoid forage legumes rather than the classical Mimosa host species (Mimosoideae) described for other Burkholderia microsymbionts . Burkholderia dilworthii strain WSM3556T was assessed for nodulation and nitrogen fixation on three separate L. ambigua genotypes (CRSLAM-37, CRSLAM-39 and CRSLAM-41) . It could nodulate and fix effectively on CRSLAM-41 but was partially effective on CRSLAM-37 and CRSLAM-39 . Moreover, WSM3556T also nodulates and fixes nitrogen in association with Lebeckia sepiaria .
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, The Root Nodulating Bacteria chapter project at the U.S. Department of Energy, Joint Genome Institute for projects of relevance to agency missions . The genome project is deposited in the Genomes OnLine Database  and the high-quality permanent draft genome sequence in IMG . Sequencing, finishing and annotation were performed by the JGI using state of the art sequencing technology . A summary of the project information is shown in Table 2.
Growth conditions and genomic DNA preparation
Burkholderia dilworthii strain WSM3556T was grown on TY solid medium  for 3 days, a single colony was selected and used to inoculate 5 ml TY broth medium. The culture was grown for 48 h on a gyratory shaker (200 rpm) at 28 °C. Subsequently 1 ml was used to inoculate 60 ml TY broth medium and grown on a gyratory shaker (200 rpm) at 28 °C until OD 0.6 was reached. DNA was isolated from 60 mL of cells using a CTAB bacterial genomic DNA isolation method . Final concentration of the DNA was 0.5 mg/ml.
Genome sequencing and assembly
The genome of Burkholderia dilworthii strain WSM3556T was sequenced at the DOE Joint Genome Institute using state of the art technology . For this genome, an Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform, which generated 9,394,768 reads totalling 2,818.4 Mbp of Illumina data. All general aspects of library construction and sequencing performed at the JGI can be found on the JGI web site . 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). The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet, version 1.1.04 , (2) 1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim , (3) Illumina reads were assembled with simulated read pairs using Allpaths (version r37348) . Parameters for assembly steps were: 1) Velvet -exp_cov 90 -cov_cutoff 20 -exportFiltered yes -very_clean yes), 2) wgsim (−e 0–1 76–2 76 -r 0 -R 0 -X 0 -d 3000 -s 300 -N 1266735), 3) Allpaths–LG (PrepareAllpathsInputs: PHRED_64 = 1 PLOIDY = 1 JUMP_COVERAGE = 25 FRAG_COVERAGE = 125, RunAllpathsLG: RUN = 125std + 25xfakedpairs TARGETS = standard VAPI_WARN_ONLY = True OVERWRITE = True). The final draft assembly contained 141 contigs in 140 scaffolds. The total size of the genome is 7.7 Mbp and the final assembly is based on 2,818.4 Mbp of Illumina draft data, which provides an average of 367x coverage of the genome.
Genes were identified using Prodigal , as part of the DOE-JGI genome annotation pipeline [23, 24] followed by a round of manual curation using GenePRIMP  for finished genomes and Draft genomes in fewer than 10 scaffolds. The predicted CDSs were translated and used to search the NCBI non-redundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. The tRNAScanSE tool  was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA . 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 . Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes-Expert Review system  developed by the Joint Genome Institute, Walnut Creek, CA, USA.
The genome is 7,679,067 nucleotides with 61.77 % GC content (Table 3) and comprised of 140 scaffolds and 141 contigs. From a total of 7,123 genes, 7,059 were protein encoding and 64 RNA only encoding genes. The majority of genes (76.25 %) were assigned a putative function whilst the remaining genes were annotated as hypothetical. The distribution of genes into COG functional categories is presented in Table 4.
Burkholderia dilworthii WSM3556T belongs to a group of Beta-rhizobia isolated from Lebeckia ambigua from the fynbos biome in South Africa . WSM3556T is phylogeneticaly most closely related to Burkholderia rhynchosiae WSM3937T and Burkholderia phytofirmans PsJNT. Of these strains only WSM3556T and WSM3937T are legume microsymbionts. Out of 13 Burkholderia strains that are known legume microsymbionts, only four (WSM3556T , WSM4176, WSM5005T , STM678T) nodulate South African papilionoid species. A comparison of these nodulating strains reveals that WSM3556T has the smallest genome (7.7 Mbp), the smallest KOG count (1295) and the lowest GC (61.77 %) percentage in this group. These four genomes share the nitrogenase-RXN MetaCyc pathway catalyzed by a multiprotein nitrogenase complex. Strains WSM3556T , WSM4176, WSM5005T  have been shown to fix nitrogen with Lebeckia ambigua provenances with varying degrees of effectiveness. WSM3556T is partially effective on two out of three L. ambigua provenances, WSM4176 is partially effective on only one L. ambigua provenance and WSM5005T is effective on all three L. ambigua provenances. The genome sequences of these fynbos bacteria provides an unprecedented opportunity to reveal the genetic determinants required for effective nitrogen fixation with Lebeckia .
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This work was performed under the auspices of the US Department of Energy 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.
The authors declare that they have no competing interests.
JH and RY supplied the strain and background information for this project, TR supplied DNA to JGI and performed all imaging, SDM and WR drafted the paper, JH provided financial support and all other authors were involved in sequencing the genome and editing the final manuscript. All authors read and approved the final manuscript.
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Cite this article
De Meyer, S.E., Tian, R., Seshadri, R. et al. High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556T . Stand in Genomic Sci 10, 64 (2015). https://doi.org/10.1186/s40793-015-0048-3
- Root-nodule bacteria
- Nitrogen fixation
- South Africa