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1.
Genome Announc ; 2(4)2014 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-25035329

RESUMO

Acinetobacter baumannii is a frequent hospital-acquired human pathogen. This report describes the draft genome sequences of two distinct A. baumannii clinical isolates from the same patient. A comparison of the genomes revealed differences in antibiotic resistance and will enable the determination of genomic differences responsible for virulence at each body site.

2.
Mol Plant Microbe Interact ; 25(3): 321-30, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22074348

RESUMO

A multilocus sequence typing (MLST) method based on allelic variation of seven chromosomal loci was developed for characterizing genotypes (GT) within the genus Bradyrhizobium. With the method, 29 distinct multilocus GT were identified among 190 culture collection soybean strains. The occupancy of 347 nodules taken from uninoculated field-grown soybean plants also was determined. The bacteroid GT were either the same as or were closely related to GT identified among strains in the culture collection. Double-nodule occupancy estimates of 2.9% were much lower than values published based on serology. Of the 347 nodules examined, 337 and 10 were occupied by Bradyrhizobium japonicum and B. elkanii, respectively. The collection strains within the species B. japonicum and B. elkaniialso were compared with Bradyrhizobium cultures from other legumes. In many cases, the observed GT varied more according to their geographic origin than by their trap hosts of isolation. In other cases, there were no apparent relationships with either the legume or geographic source. The MLST method that was developed should be a useful tool in determining the influence of geographic location, temperature, season, soil type, and host plant cultivar on the distribution of GT of Bradyrhizobium spp.


Assuntos
Técnicas de Tipagem Bacteriana/métodos , Bradyrhizobium/classificação , Glycine max/microbiologia , Tipagem de Sequências Multilocus/métodos , Nódulos Radiculares de Plantas/microbiologia , Sequência de Bases , Bradyrhizobium/genética , Bradyrhizobium/isolamento & purificação , Bradyrhizobium/fisiologia , Primers do DNA/genética , DNA Bacteriano/química , DNA Bacteriano/genética , Evolução Molecular , Variação Genética , Genótipo , Geografia , Dados de Sequência Molecular , Filogenia , Glycine max/fisiologia , Simbiose
3.
Appl Environ Microbiol ; 76(12): 3967-77, 2010 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-20418433

RESUMO

A multilocus sequence typing (MLST) analysis was used to examine the genetic structure and diversity within the two large extrachromosomal replicons in Medicago-nodulating rhizobia (Sinorhizobium meliloti and Sinorhizobium medicae). The allelic diversity within these replicons was high compared to the reported diversity within the corresponding chromosomes of the same strains (P. van Berkum et al., J. Bacteriol. 188:5570-5577, 2006). Also, there was strong localized linkage disequilibrium (LD) between certain pSymA loci: e.g., nodC and nifD. Although both of these observations could be explained by positive (or diversifying) selection by plant hosts, results of tests for positive selection did not provide consistent support for this hypothesis. The strong LD observed between the nodC and nifD genes could also be explained by their close proximity on the pSymA replicon. Evidence was obtained that some nodC alleles had a history of intragenic recombination, while other alleles of this locus had a history of intergenic recombination. Both types of recombination were associated with a decline in symbiotic competence with Medicago sativa as the host plant. The combined observations of LD between the nodC and nifD genes and intragenic recombination within one of these loci indicate that the symbiotic gene region on the pSymA plasmid has evolved as a clonal segment, which has been laterally transferred within the natural populations.


Assuntos
Impressões Digitais de DNA , Variação Genética , Medicago sativa/microbiologia , Plasmídeos , Sinorhizobium/genética , Proteínas de Bactérias/genética , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , Desequilíbrio de Ligação , Dados de Sequência Molecular , N-Acetilglucosaminiltransferases/genética , Fixação de Nitrogênio , Recombinação Genética , Análise de Sequência de DNA , Homologia de Sequência , Sinorhizobium/fisiologia , Simbiose
4.
Appl Environ Microbiol ; 73(23): 7597-604, 2007 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-17921275

RESUMO

Multilocus sequence typing (MLST) is a sequence-based method used to characterize bacterial genomes. This method was used to examine the genetic structure of Medicago-nodulating rhizobia at the Amra site, which is located in an arid region of Tunisia. Here the annual medics Medicago laciniata and M. truncatula are part of the natural flora. The goal of this study was to identify whether distinct chromosomal groups of rhizobia nodulate M. laciniata because of its restricted requirement for specific rhizobia. The MLST analysis involved determination of sequence variation in 10 chromosomal loci of 74 isolates each of M. laciniata and M. truncatula. M. truncatula was used as a control trap host, because unlike M. laciniata, it has relatively unrestricted rhizobial requirements. Allelic diversity among the plasmid nodC alleles in the isolates was also determined. The 148 isolates were placed into 26 chromosomal sequence types (STs), only 3 of which had been identified previously. The rhizobia of M. laciniata were shown to be part of the general Medicago-nodulating population in the soil because 99.95% of the isolates had chromosomal genotypes similar to those recovered from M. truncatula. However, the isolates recovered from M. laciniata were less diverse than those recovered from M. truncatula, and they also harbored an unusual nodC allele. This could perhaps be best explained by horizontal transfer of the different nodC alleles among members of the Medicago-nodulating rhizobial population at the field site. Evidence indicating a history of lateral transfer of rhizobial symbiotic genes across distinct chromosomal backgrounds is provided.


Assuntos
Medicago truncatula/microbiologia , Medicago/microbiologia , Rhizobium/genética , Simbiose/genética , Alelos , Proteínas de Bactérias/genética , Cromossomos Bacterianos/genética , Variação Genética , Genoma Bacteriano , Genótipo , Dados de Sequência Molecular , N-Acetilglucosaminiltransferases/genética , Filogenia , Rhizobium/classificação , Rhizobium/crescimento & desenvolvimento , Análise de Sequência de DNA , Tunísia
5.
J Bacteriol ; 188(15): 5570-7, 2006 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-16855247

RESUMO

Multilocus sequence typing (MLST), a sequence-based method to characterize bacterial genomes, was used to examine the genetic structure in a large collection of Medicago-nodulating rhizobial strains. This is the first study where MLST has been applied in conjunction with eBURST analysis to determine the population genetic structure of nonpathogenic bacteria recovered from the soil environment. Sequence variation was determined in 10 chromosomal loci of 231 strains that predominantly originated from southwest Asia. Genetic diversity for each locus ranged from 0.351 to 0.819, and the strains examined were allocated to 91 different allelic profiles or sequence types (STs). The genus Medicago is nodulated by at least two groups of rhizobia with divergent chromosomes that have been classified as Sinorhizobium meliloti and Sinorhizobium medicae. Evidence was obtained that the degree of genetic exchange among the chromosomes across these groups is limited. The symbiosis with Medicago polymorpha of nine strains placed in one of these groups, previously identified as S. medicae, ranged from ineffective to fully effective, indicating that there was no strong relationship between symbiotic phenotype and chromosomal genotype.


Assuntos
Genoma Bacteriano , Medicago/microbiologia , Rhizobiaceae/genética , Alelos , Sudeste Asiático , Variação Genética , Dados de Sequência Molecular , Análise de Sequência , Sinorhizobium/genética , Sinorhizobium/fisiologia , Microbiologia do Solo , Simbiose
6.
Syst Appl Microbiol ; 29(3): 207-15, 2006 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-16564957

RESUMO

The symbiotic bradyrhizobia of Aeschynomene indica and the aquatic budding bacterium Blastobacter denitrificans have much in common and this study broadens the characters that are shared between the two. The 23S rRNA gene sequences of the bradyrhizobial isolates were most similar to each other and to the sequence of Bl. denitrificans. Evidence for the presence of photosynthetic genes in the genome of Bl. denitrificans was obtained by PCR using primers to the conserved M subunit (pufM) of the photosynthetic reaction center present in purple sulfur and purple nonsulfur bacteria. The deduced amino acid sequences of the partial PufM protein of Bl. denitrificans and the corresponding sequences obtained from the bradyrhizobial isolates were identical. Both the bradyrhizobial isolates and the type strain of Bl. denitrificans shared the ability to propagate by budding, demonstrated by electron microscopy. Even though many interspecific characters were shared among the bradyrhizobial isolates including Bl. denitrificans, it was evident from Amplified Fragment Length Polymorphism (AFLP) analysis that genomic variation existed among the collection that was examined. Variation among bradyrhizobial isolates and Bl. denitrificans also was established in carbon and nitrogen source utilization and the ability to grow at elevated temperature. Based on these results and previously reported evidence it is suggested that the type strain for Bl. denitrificans and the bradyrhizobial isolates from nodules of A. indica belong to a common group of bacteria. Therefore, it is proposed that they be combined into the genus Bradyrhizobium and that LMG 8443 be transferred to this genus as the type strain for B. denitrificans.


Assuntos
Bradyrhizobiaceae/classificação , Bradyrhizobium/classificação , Bradyrhizobiaceae/genética , Bradyrhizobium/genética , Bradyrhizobium/ultraestrutura , Fabaceae/microbiologia , Microscopia Eletrônica , Dados de Sequência Molecular , Fixação de Nitrogênio , RNA Ribossômico 23S/química , Simbiose
7.
J Bacteriol ; 185(10): 2988-98, 2003 May.
Artigo em Inglês | MEDLINE | ID: mdl-12730157

RESUMO

It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.


Assuntos
DNA Intergênico , Filogenia , RNA Ribossômico 16S , RNA Ribossômico 23S , Rhizobiaceae/genética , Sequência de Bases , Evolução Molecular , Conversão Gênica , Funções Verossimilhança , Dados de Sequência Molecular , Reação em Cadeia da Polimerase/métodos , Polimorfismo Genético , Recombinação Genética , Rhizobiaceae/fisiologia , Homologia de Sequência do Ácido Nucleico
8.
Appl Environ Microbiol ; 68(3): 1132-6, 2002 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-11872460

RESUMO

Blastobacter spp. are freshwater bacteria that form rosette structures by cellular attachment to a common base. Comparative analyses of ribosomal 16S rRNA gene and internally transcribed spacer region sequences indicated that B. denitrificans is a member of the alpha-subdivision of Proteobacteria. Among the alpha-Proteobacteria, B. denitrificans was related to a cluster of genera, including Rhodopseudomonas palustris, Afipia felis, Nitrobacter hamburgensis, and Bradyrhizobium spp. Although the precise phylogenetic relationships among these genera could not be established with a high degree of confidence, the sequences of B. denitrificans and several bradyrhizobial isolates from nodules of Aeschynomene indica were almost identical. Bradyrhizobia are bacteria that form nitrogen-fixing symbioses with legumes, including soybeans (Glycine max) and members of the genus Aeschynomene. From symbiotic infectiveness tests we demonstrated that the type strain for B. denitrificans, IFAM 1005, was capable of forming an effective nitrogen-fixing symbiosis with A. indica. Not only do these results reveal a previously unknown ecological adaptation of a relatively obscure aquatic bacterium, but they also demonstrate how evidence gathered from molecular systematic analyses can sometimes provide clues for predicting ecological behavior.


Assuntos
Fabaceae/microbiologia , Água Doce/microbiologia , Fixação de Nitrogênio , Rhizobiaceae/classificação , Simbiose , DNA Espaçador Ribossômico/genética , Evolução Molecular , Dados de Sequência Molecular , Filogenia , RNA Ribossômico 16S/genética , Rhizobiaceae/genética , Rhizobiaceae/crescimento & desenvolvimento , Análise de Sequência de DNA , Glycine max/microbiologia
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