Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471

Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-(N-2) fixing root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce growing at Oyster Harbour, Albany district, Western Australia in 1982. This strain is in commercial production as an inoculant for Lupinus and Ornithopus. Here we describe the features of Bradyrhizobium sp. strain WSM471, together with genome sequence information and annotation. The 7,784,016 bp high-quality-draft genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program

Genome sequence of the Lebeckia ambigua-nodulating 'Burkholderia sprentiae' strain WSM5005T

"Burkholderia sprentiae" strain WSM5005(T) is an aerobic, motile, Gram-negative, non-sporeforming rod that was isolated in Australia from an effective N-2-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of "Burkholderia sprentiae" strain WSM5005T, together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program

Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum

Rhizobium leguminosarum bv. trifolii is a soil-inhabiting bacterium that has the capacity to be an effective N2-fixing microsymbiont of Trifolium (clover) species. R. leguminosarum bv. trifolii strain WSM1689 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Trifolium uniflorum collected on the edge of a valley 6 km from Eggares on the Greek Island of Naxos. Although WSM1689 is capable of highly effective N2-fixation with T. uniflorum, it is either unable to nodulate or unable to fix N2 with a wide range of both perennial and annual clovers originating from Europe, North America and Africa. WSM1689 therefore possesses a very narrow host range for effective N2 fixation and can thus play a valuable role in determining the geographic and phenological barriers to symbiotic performance in the genus Trifolium. Here we describe the features of R. leguminosarum bv. trifolii strain WSM1689, together with the complete genome sequence and its annotation. The 6,903,379 bp genome contains 6,709 protein-coding genes and 89 RNA-only encoding genes. This multipartite genome contains six distinct replicons; a chromosome of size 4,854,518 bp and five plasmids of size 667,306, 518,052, 341,391, 262,704 and 259,408 bp. This rhizobial genome is one of 20 sequenced as part of a DOE Joint Genome Institute 2010 Community Sequencing Program

Genome sequence of <i>Ensifer medicae</i> strain WSM1369; an effective microsymbiont of the annual legume <i>Medicago sphaerocarpos</i>

Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy). WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369, together with genome sequence information and its annotation. The 6,402,557 bp standard draft genome is arranged into 307 scaffolds of 307 contigs containing 6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project

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

Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-sporeforming rod that was isolated from an effective nitrogen (N-2) 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

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

Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-sporeforming rod that was isolated from an effective nitrogen (N-2) 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

Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1

Rhizobium leguminosarum bv. trifolii strain TA1 is an aerobic, motile, Gram-negative, non-spore-forming rod that is an effective nitrogen fixing microsymbiont on the perennial clovers originating from Europe and the Mediterranean basin. TA1 however is ineffective with many annual and perennial clovers originating from Africa and America. Here we describe the features of R. leguminosarum bv. trifolii strain TA1, together with genome sequence information and annotation. The 8,618,824 bp high-quality-draft genome is arranged in a 6 scaffold of 32 contigs, contains 8,493 protein-coding genes and 83 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program

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

Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N(2)) fixing root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this microsymbiont is a poorly effective N(2) 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 N(2) 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

Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements

Tripartite integrative and conjugative elements (ICE3) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE3 regions of M. ciceri WSM1271 ICEMcSym1271 combine and excise to form a single circular element. This assembly requires three coordinated recombination events involving three site-specific recombinases IntS, IntG and IntM. Here, we demonstrate that three excisionases–or recombination directionality factors—RdfS, RdfG and RdfM are required for ICE3 excision. Transcriptome sequencing revealed that expression of ICE3 transfer and conjugation genes was induced by quorum sensing. Quorum sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a “master controller” of ICE3 assembly and excision. The dependence of all three excisive reactions on RdfS ensures that ICE3 excision occurs via a stepwise sequence of recombination events that avoids splitting the chromosome into a non-viable configuration. These discoveries expose a surprisingly simple control system guiding molecular assembly of these novel and complex mobile genetic elements and highlight the diverse and critical functions of excisionase proteins in control of horizontal gene transfer

Why are the symbioses between some genotypes of Sinorhizobium and Medicago suboptimal for N2 fixation?

The conversion of atmospheric dinitrogen (N2) into plant available nitrogen (N), by legumes and their prokaryotic microsymbionts, is an integral component of sustainable farming. A key constraint to increasing the amount of N2 fixed in agricultural systems is the prevalence of symbioses which fix little or no N. The biotic factors leading to this suboptimal N2 fixation have not been extensively analysed. Using the widely studied and cultivated perennial legume Medicago sativa and the model indeterminate annual legume Medicago truncatula with the sequenced bacterial microsymbiont Sinorhizobium meliloti 1021 (Sm1021) as a basis, the work presented in this thesis examined the effectiveness of N2 fixation in these associations and in other comparable systems and investigated factors which lead to the establishment of suboptimally effective symbioses. The ability of Sm1021, S. medicae WSM419 and the uncharacterised Sinorhizobium sp. WSM1022 to fix N with M. truncatula A17, M. sativa cv. Sceptre and a range of other Medicago spp. was evaluated in N-limited conditions. As measured by plant shoot dry weights and N-content, Sm1021 was partially effective with M. truncatula A17 whereas WSM1022 and WSM419 were both effective with this host in comparison to nitrogen-fed (N-fed) control plants. In contrast, Sm1021 and WSM1022 were effective with M. sativa while WSM419 was only partially effective. Nodules induced by Sm1021 on M. truncatula A17 were more numerous, paler, smaller in size and more widely distributed over the entire root system than in the two effective symbioses with this host. On the contrary, nodule number, size and distribution did not differ between these three strains on M. sativa. WSM1022 was effective on M. littoralis, M. tornata and two other cultivars of M. truncatula (Jemalong and Caliph) but Sm1021 was only partially effective on these hosts. These data indicate that the model indeterminate legume symbiosis between M. truncatula and Sm1021 is not optimally matched for N2 fixation and that Sm1021 possesses broader symbiotic deficiencies. In addition, the interaction of WSM1022 with M. polymorpha (small white nodules but does not fix N), M. murex (does not nodulate), M. arabica (partially effective N2 fixation) and M. sphaeorcarpus (partially effective N2 fixation), and the sequence of the 16S rDNA, are all consistent with this isolate belonging to the species S. meliloti. The colony morphology of TY, half-LA and YMA agar plate cultures of Sm1021, WSM419 and WSM1022 suggested differences in EPS profiles between these strains. Sm1021 is very dry, compared to the mucoid WSM419 and extremely mucoid WSM1022. Sm1021 is known to carry an insertion in expR rendering the gene non-functional and resulting in the dry colony phenotype. WSM419 has an intact copy of expR, while the expR status of WSM1022 is not known. Rm8530, a spontaneous mucoid derivative of Sm1021 with an intact expR, was significantly less effective with M. truncatula than Sm1021, but there was no difference in effectiveness between these strains on M. sativa. The effectiveness of Sm1021, when complemented with a plasmid-borne copy of expR from Rm8530, was significantly reduced on M. truncatula but not M. sativa, implicating a functional expR as being the cause of reduced N2 fixation observed with Rm8530 on M. truncatula. ExpR could reduce the effectiveness of Rm8530 by acting as a negative regulator of genes essential for symbiosis with M. truncatula, or by altering the quantity or structure of succinoglycan and/or galactoglucan produced. These data support the emerging view of ExpR being a central regulator of numerous cellular processes. The timing of nodulation between Sm1021 and WSM419 on M. truncatula and M. sativa was investigated. Compared to the other symbioses analysed, the appearance of nodule initials and nodules was delayed when M. truncatula was inoculated with Sm1021 by 3 and 4 days, respectively. To explore whether events during early symbiotic signalling exchange could account for these observed delays, leading to the establishment of a suboptimal N2-fixing symbiosis, a novel system was developed to compare the response of the Sm1021 transcriptome to roots and root exudates of M. truncatula A17 and M. sativa cv. Sceptre. This system consisted of a sealed 1 L polycarbonate chamber containing a stainless steel tripod with a wire mesh platform on which surface-sterilised seeds could be placed and allowed to germinate through the mesh, into a hydroponic medium below. After germination, Sm1021 cells were inoculated into the hydroponic solution, exposed to the roots and root exudates for 16 h, harvested and their RNA extracted. Comparison of Sm1021 mRNA from systems exposed to M. truncatula or M. sativa revealed marked differences in gene expression between the two. Compared to the no plant control, when M. sativa was the host plant, 23 up-regulated and 40 down-regulated Sm1021 genes were detected, while 28 up-regulated and 45 down-regulated genes were detected with M. truncatula as the host. Of these, 12 were up-regulated and 28 were down-regulated independent of whether M. truncatula or M. sativa was the host. Genes expressed differently when exposed to either M. truncatula or M. sativa included nex18, exoK, rpoE1 and a number of other genes coding for either hypothetical proteins or proteins with putative functions including electron transporters and ABC transporters. Characterisation of these differentially expressed genes along with a better understanding of the composition of M. truncatula root exudates would yield a clearer insight into the contribution of early signal exchange to N2 fixation. Comparison of the regulation of nodule number between Sm1021 and WSM419 on M. truncatula and M. sativa revealed nodule initials at 42 days post-inoculation (dpi) on M. truncatula inoculated with Sm1021. In contrast, no new nodule initials were present 21 dpi on any of the other interactions examined. Moreover, analysis of nodule sections revealed that the number of infected cells in M. truncatula-Sm1021 nodules was less than for comparable symbioses. These data suggest that nodule number is not tightly controlled in the M. truncatula-Sm1021 association, probably due to N2 fixation being insufficient to trigger the down regulation of nodulation. Quantification of N2 fixation activity in this and other more effective symbioses is required. The poor effectiveness of the M. truncatula-Sm1021 symbiosis makes these organisms unsuitable as the model indeterminate interaction and the implications for legume research are discussed. The recently sequenced WSM419 strain, revealed here to fix N2 more effectively with M. truncatula than Sm1021, may be a better model microsymbiont, although WSM419 is only partially effective for N2 fixation with M. sativa. The sequencing of S. meliloti WSM1022, a highly effective strain with both M. truncatula and M. sativa, would provide a valuable resource in indentifying factors which preclude the establishment of effective symbioses