Rapid in situ evolution of nodulating strains for Biserrula pelecinus L. through lateral transfer of a symbiosis island from the original mesorhizobial inoculant

Diverse rhizobia able to nodulate Biserrula pelecinus evolved following in situ transfer of nodA and nifH from an inoculant to soil bacteria. Transfer of these chromosomal genes and the presence of an identical integrase gene adjacent to a Phe tRNA gene in both the inoculant and recipients indicate that there was lateral transfer of a symbiosis island

Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419

Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome se-quence for a microsymbiont of the group of annual medic species adapted to acid soils. We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes. The genome contains a chromosome of size 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp. The smallest plasmid is a fea-ture unique to this medic microsymbiont

Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia

Biserrula pelecinus L. is a pasture legume that was introduced to Australia from the Mediterranean basin in 1993. Although the native rhizobial population could not nodulate B. pelecinus at the time of its introduction, recent research has shown the emergence of a diversity of strains (novel isolates) that are able to do so. Three novel isolates, WSM2073T, WSM2074 and WSM2076, had nearly identical 16S rRNA gene sequences, and clustered separately with all recognized species of the genus Mesorhizobium. Conversely, the novel isolate WSM2075T had >23 nt mismatches with the above three isolates. All four novel isolates shared 97-99% 16S rRNA gene sequence similarity with the type strains of all recognized Mesorhizobium species. However, strains WSM2073T, WSM2074 and WSM2076 showed <95.2% dnaK gene sequence similarity to the type strains of recognized Mesorhizobium species, and <92.9% to WSM2075T (which also shared <95.5% dnaK gene sequence similarity to the type strains of recognized Mesorhizobium species). Results for GSII gene sequencing were consistent with those for the dnaK gene. The fatty acid profiles of the novel isolates were diagnostic of root-nodule bacteria, but did not match those of recognized bacterial species. Strain WSM2075T had a significantly different fatty acid profile from the other three isolates. The above results indicated that strains WSM2073T, WSM2074 and WSM2076 represent the same species. Strain WSM2073T showed <45% DNA-DNA relatedness and WSM2075T <50% DNA-DNA relatedness with the type strains of recognized Mesorhizobium species; these two novel isolates shared 59% DNA-DNA relatedness. Collectively, these data indicate that strains WSM2073T, WSM2074 and WSM2076, and strain WSM2075T belong to two novel species of the genus Mesorhizobium, for which the names Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov. are proposed, respectively. The type strain of Mesorhizobium australicum sp. nov. is WSM2073T (=LMG 24608T=HAMBI 3006T) and the type strain of Mesorhizobium opportunistum sp. nov. is WSM2075T (=LMG 24607T=HAMBI 3007T)

Characterisation of root-nodule bacteria isolated from perennial Southern African species of Lotononis

Lotononis is a genus of approximately 150 shrubs, herbaceous perennials and annuals belonging to the subfamily Fabaceae (Van Wyk, 1991). They are distributed mainly in southern Africa, with some species extending throughout Africa, southern Spain, Turkey, south-eastern Bulgaria and part of the Arabian Peninsula to the north-west of the Indian sub-continent (Van Wyk, 1991). Lotononis species have shown potential as perennial pasture legumes that can be used to help reduce the risk of dryland salinity in southern Australian agricultural systems. Species in the section Listia in particular may be useful as pasture legumes as they are perennial, stoloniferous, and lack the poisonous cyanogenic or alkaloid compounds found in some species of Lotononis. L. bainesii, from the Listia section, has been shown to grow well in southern Australia (Roberts & Carbon, 1969) and will grow on acid, sandy soils (R. Yates, pers. comm.). L. bainesii is nodulated by pink-pigmented root-nodule bacteria. Jaftha et al. (2002) characterised nine L. bainesii isolates and found them to be related to Methylobacterium. The genus Methylobacterium, often referred to as pink-pigmented facultative methylotrophs (PPFMs), are capable of growth on C1 compounds such as formate and methanol as sole carbon sources. PPFMs are ubiquitous in the plant phyllosphere and rhizosphere, where they utilize methanol and other C1 compounds that are the products of plant metabolism (Trotsenko et al, 2001). They can promote the germination or the growth of plants, probably because of their ability to synthesise auxins, cytokinins and other plant growth promoting substances (Holland & Polacco, 1994; Ivanova et al., 2000; Trotsenko et al., 2001). However, until the paper by Sy et al. (2001), describing Methylobacterium nodulans, which was isolated from nodules of Crotalaria species found in Senegal, no Methylobacterium species had been known to nodulate legumes, or indeed to fix nitrogen. The objectives in this study were to characterise root-nodule bacteria isolated from four species from the Listia section of Lotononis (L. angolensis, L. bainesii, L. listii and L. solitudinis) using a range of phenotypic and genetic techniques

New understandings in microbial (bacterial) evolution - A review

This review addresses the impact of the coming avalanche of genomic data and the convergence of fresh ideas on evolution on the pre-genetic concepts on bacterial evolution. The context is set with a brief historical account of the discovery of microbes and what Darwin wrote about them. The need to view bacterial evolution afresh in the 21st century is discussed. Current understanding of evolutionary forces and evolutionary mechanisms occurring in bacteria are outlined and secrets to the rapid evolution of bacteria are revealed. We conclude that the budding image of bacteria as gene-swapping entities stipulates a revision of such concepts as organism, species and evolution itself and propose a hypothesis that a bacterium is a 'composite entity' with a multiple decent of origin

A basis for the development of an inferior N2 fixation phenotype in root nodule bacteria following lateral transfer of symbiotic genes

Symbiotic N2 fixation by root nodule bacteria (RNB) plays a significant role in world agricultural productivity by annually converting in excess of 120 million tonnes of atmospheric N2 into ammonia. A successful symbiotic interaction requires compatibility between the RNB and the legume at many different stages, from initial recognition, through successful differentiation to nitrogen fixation. All these processes are complex and require the regulation and function of multiple genes/gene families in both partners

Selfish Islands and converging plasmids - new insights into evolution of root nodule bacteria

The coming avalanche of genomic data is bringing opportunities for new insights into the genome architecture and evolution of root nodule bacteria. Comparative genomic analyses of root nodule bacteria reveal that mobile genetic elements ranging from transposons, integrons, genomic islands and plasmids are widespread in these genomes. Genomic islands are plasmid-like DNA regions that are integrated into prokaryotic chromosomes and confer a variety of functions (resistance, degradation, metabolism, pathogenicity, secretion and symbiosis) to the host genome. Acquisition can extend the capacity of the host bacterium to adapt to new environments. Genomic islands that confer nitrogen fixation capacity to non symbiotic bacteria are termed 'symbiosis islands' because they carry nodulation and nitrogen fixation genes required for the legume symbiosis as well as genes required for the excision, insertion and transfer of the island

Root-nodule bacteria from indigenous legumes in the north-west of Western Australia and their interaction with exotic legumes

Bacteria were isolated from root-nodules collected from indigenous legumes at 38 separate locations in the Gascoyne and Pilbara regions of Western Australia. Authentication of cultures resulted in 31 being ascribed status as root-nodule bacteria based upon their nodulation of at least one of eight indigenous legume species. The authenticated isolates originated from eight legume genera from 19 sites. Isolates were characterised on the basis of their growth and physiology; 20 isolates were fast-growing and 11 were slow-growing (visible growth within 3 and 7d, respectively). Fast-growers were isolated from Acacia, Isotropis, Lotus and Swainsona, whilst slow-growers were from Muelleranthus, Rhynchosia and Tephrosia. Indigofera produced one fast-growing isolate and seven slow-growing isolates. Three indigenous legumes (Swainsona formosa, Swainsona maccullochiana and Swainsona pterostylis) nodulated with fast-growing isolates and four species (Acacia saligna, Indigofera brevidens, Kennedia coccinea and Kennedia prorepens) nodulated with both fast- and slow-growing isolates. Swainsona kingii did not form nodules with any isolates. Fast-growing isolates were predominantly acid-sensitive, alkaline- and salt-tolerant. All slow-growing isolates grew well at pH 9.0 whilst more than half grew at pH 5.0, but all were salt-sensitive. All isolates were able to grow at 37deg;C. The fast-growing isolates utilised disaccharides, whereas the slow-growing isolates did not. Symbiotic interactions of the isolates were assessed on three annual, one biennial and nine perennial exotic legume species that have agricultural use, or potential use, in southern Australia. Argyrolobium uniflorum, Chamaecytisus proliferus, Macroptilium atropurpureum, Ononis natrix, Phaseolus vulgaris and Sutherlandia microphylla nodulated with one or more of the authenticated isolates. Hedysarum coronarium, Medicago sativa, Ornithopus sativus, Ornithopus compressus, Trifolium burchellianum, Trifolium polymorphum and Trifolium uniflorum did not form nodules. Investigation of the 31 authenticated isolates by polymerase chain reaction with three primers resulted in the RPO1 primer distinguishing 20 separate banding patterns, while ERIC and PucFor primers distinguished 26 separate banding patterns. Sequencing the 16S rRNA gene for four fast- and two slow-growing isolates produced the following phylogenetic associations; WSM1701 and WSM1715 (isolated from Lotus cruentus and S. pterostylis, respectively) displayed 99% homology with Sinorhizobium meliloti, WSM1707 and WSM1721 (isolated from Sinorhizobium leeana and Indigofera sp., respectively) displayed 99% homology with Sinorhizobium terangae, WSM1704 (isolated from Tephrosia gardneri) shared 99% sequence homology with Bradyrhizobium elkanii, and WSM1743 (isolated from Indigofera sp.) displayed 99% homology with Bradyrhizobium japonicum