Phylogenetic Analysis of
            <i>Bradyrhizobium japonicum</i>
            and Photosynthetic Stem-Nodulating Bacteria from
            <i>Aeschynomene</i>
            Species Grown in Separated Geographical Regions

Wong, Frank; Stackebrandt, Erko; Ladha, J. K.; Fleischman, Darrell; Date, R. A.; Fuerst, John A.

doi:10.1128/aem.60.3.940-946.1994

Cited by 61 publications

(27 citation statements)

References 38 publications

(29 reference statements)

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“…The position and orientation of highly conserved chromosomal genes and integrase genes derived from accessory elements such as plasmids or bacteriophages may favour fusion and excision events among genes and chromosomes as well as between large replicons in alpha Proteobacteria [25,47,111,112]. Finally, the close phylogeny of B. japonicum with the bacteriochlorophyll a containing Bradhyrhizobium species [65], supports the idea that essential genetic information needed to conduct photosynthesis was lost in many Bradyrhizobium strains. The rational for this is that photosynthesis is too complex to be acquired independently at di¡erent branching points during bacterial evolution [5^7].…”

Section: Small and Large Genomesmentioning

confidence: 77%

“…chvA and chvB homologous to A. tumefaciens genes) for the early phases during plant colonisation in the di¡erent plant-associated bacteria [50]. Two of the remarkable characteristics of plant-associated bacteria are their high genetic diversity found world-wide and their clonal population structure encountered in speci¢c ecosystems [52,56,64,65].…”

Section: Local Adaptations and Plasmidsmentioning

confidence: 99%

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Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome?

Moreno

1998

FEMS Microbiology Reviews

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Animal intracellular Proteobacteria of the alpha subclass without plasmids and containing one or more chromosomes are phylogenetically entwined with opportunistic, plant-associated, chemoautotrophic and photosynthetic alpha Proteobacteria possessing one or more chromosomes and plasmids. Local variations in open environments, such as soil, water, manure, gut systems and the external surfaces of plants and animals, may have selected alpha Proteobacteria with extensive metabolic alternatives, broad genetic diversity, and more flexible and larger genomes with ability for horizontal gene flux. On the contrary, the constant and isolated animal cellular milieu selected heterotrophic alpha Proteobacteria with smaller genomes without plasmids and reduced genetic diversity as compared to their plant-associated and phototrophic relatives. The characteristics and genome sizes in the extant species suggest that a second chromosome could have evolved from megaplasmids which acquired housekeeping genes. Consequently, the genomes of the animal cell-associated Proteobacteria evolved through reductions of the larger genomes of chemoautotrophic ancestors and became rich in adenosine and thymidine, as compared to the genomes of their ancestors. Genome organisation and phylogenetic ancestor-descendent relationships between extant bacteria of closely related genera and within the same monophyletic genus and species suggest that some strains have undergone transition from two chromosomes to a single replicon. It is proposed that as long as the essential information is correctly expressed, the presence of one or more chromosomes within the same genus or species is the result of contingency. Genetic drift in clonal bacteria, such as animal cell-associated alpha Proteobacteria, would depend almost exclusively on mutation and internal genetic rearrangement processes. Alternatively, genomic variations in reticulate bacteria, such as many intestinal and plant cell-associated Proteobacteria, will depend not only on these processes, but also on their genetic interactions with other bacterial strains. Common pathogenic domains necessary for the invasion and survival in association with cells have been preserved in the chromosomes of the animal and plant-associated alpha Proteobacteria. These pathogenic domains have been maintained by vertical inherence, extensively ameliorated to match the chromosome G + C content and evolved within chromosomes of alpha Proteobacteria.

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Section: Small and Large Genomesmentioning

confidence: 77%

Section: Local Adaptations and Plasmidsmentioning

confidence: 99%

Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome?

Moreno

1998

FEMS Microbiology Reviews

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“…(A. indica) (59). This was later confirmed by additional 16S rRNA gene sequencing of other photosynthetic rhizobia (47,55) and by fatty acid analysis (47). Additional data came from numerical taxonomy (150 phenotypic characteristics) indicating that the photosynthetic rhizobia constitute a unique phenon that could be considered distinct from Bradyrhizobium (33).…”

mentioning

confidence: 83%

“…Since the different reports on Aeschynomene bradyrhizobia generally studied different rhizobium collections and focused on either nodulation (1), phylogeny (55), or photosynthesis (48), the data appeared fragmentary and did not allow a com-prehensive view of the diversity and evolution of Bradyrhizobium isolates from Aeschynomene species. Our objective was thus to examine possible links among the presence of photosynthetic pigments, nodulation capacity, and 16S rRNA genebased phylogeny among bradyrhizobia from Aeschynomene species.…”

mentioning

confidence: 99%

Photosynthetic Bradyrhizobia from Aeschynomene spp. Are Specific to Stem-Nodulated Species and Form a Separate 16S Ribosomal DNA Restriction Fragment Length Polymorphism Group

Molouba¹,

Lorquin²,

Willems

et al. 1999

Appl Environ Microbiol

104

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We obtained nine bacterial isolates from root or collar nodules of the non-stem-nodulated Aeschynomene species A. elaphroxylon, A. uniflora, or A. schimperi and 69 root or stem nodule isolates from the stem-nodulated Aeschynomene species A. afraspera, A. ciliata, A. indica,A. nilotica, A. sensitiva, and A. tambacoundensis from various places in Senegal. These isolates, together with 45 previous isolates from variousAeschynomene species, were studied for host-specific nodulation within the genus Aeschynomene, also revisiting cross-inoculation groups described previously by D. Alazard (Appl. Environ. Microbiol. 50:732–734, 1985). The whole collection ofAeschynomene nodule isolates was screened for synthesis of photosynthetic pigments by spectrometry, high-pressure liquid chromatography, and thin-layer chromatography analyses. The presence ofpuf genes in photosyntheticAeschynomene isolates was evidenced both by Southern hybridization with a Rhodobacter capsulatus photosynthetic gene probe and by DNA amplification with primers defined from photosynthetic genes. In addition, amplified 16S ribosomal DNA restriction analysis was performed on 45 Aeschynomeneisolates, including strain BTAi1, and 19 reference strains fromBradyrhizobium japonicum, Bradyrhizobium elkanii, and other Bradyrhizobium sp. strains of uncertain taxonomic positions. The 16S rRNA gene sequence of the photosynthetic strain ORS278 (LMG 12187) was determined and compared to sequences from databases. Our main conclusion is that photosynthetic Aeschynomene nodule isolates share the ability to nodulate particular stem-nodulated species and form a separate subbranch on the Bradyrhizobium rRNA lineage, distinct from B. japonicum and B. elkanii.

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“…From a phylogenetic point of view, stem‐nodulating Aeschynomene symbionts belong to the genus Bradyrhizobium (Wong et al. , 1994), but form a separate sub‐branch distinct from the non‐photosynthetic species, Bradyrhizobium japonicum and B. elkanii (Molouba et al.…”

Section: Introductionmentioning

confidence: 99%

Diversity analyses of Aeschynomene symbionts in Tropical Africa and Central America reveal that nod‐independent stem nodulation is not restricted to photosynthetic bradyrhizobia

Miché

Moulin

Chaintreuil

et al. 2010

Environmental Microbiology

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SummaryTropical aquatic legumes of the genus Aeschynomene are unique in that they can be stem-nodulated by photosynthetic bradyrhizobia. Moreover, a recent study demonstrated that two Aeschynomene indica symbionts lack canonical nod genes, thereby raising questions about the distribution of such atypical symbioses among rhizobial-legume interactions. Population structure and genomic diversity were compared among stem-nodulating bradyrhizobia isolated from various Aeschynomene species of Central America and Tropical Africa. Phylogenetic analyses based on the recA gene and whole-genome amplified fragment length polymorphism (AFLP) fingerprints on 110 bacterial strains highlighted that all the photosynthetic strains form a separate cluster among bradyrhizobia, with no obvious structuring according to their geographical or plant origins. Nod-independent symbiosis was present in all sampling areas and seemed to be linked to Aeschynomene host species. However, it was not strictly dependent on photosynthetic ability, as exemplified by a newly identified cluster of strains that lacked canonical nod genes and efficiently stemnodulated A. indica, but were not photosynthetic. Interestingly, the phenotypic properties of this new cluster of bacteria were reflected by their phylogenetical position, as being intermediate in distance between classical root-nodulating Bradyrhizobium spp. and photosynthetic ones. This result opens new prospects about stem-nodulating bradyrhizobial evolution.

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Phylogenetic Analysis of Bradyrhizobium japonicum and Photosynthetic Stem-Nodulating Bacteria from Aeschynomene Species Grown in Separated Geographical Regions

Cited by 61 publications

References 38 publications

Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome?

Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome?

Photosynthetic Bradyrhizobia from Aeschynomene spp. Are Specific to Stem-Nodulated Species and Form a Separate 16S Ribosomal DNA Restriction Fragment Length Polymorphism Group

Diversity analyses of Aeschynomene symbionts in Tropical Africa and Central America reveal that nod‐independent stem nodulation is not restricted to photosynthetic bradyrhizobia

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