Pablo Vinuesa | Universidad Nacional Autónoma de México (original) (raw)

Papers by Pablo Vinuesa

Research paper thumbnail of Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

Front. Microbiol., 2017

The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotro... more The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic

Research paper thumbnail of Complete Genome Sequencing of Stenotrophomonas acidaminiphila ZAC14D2_NAIMI4_2, a Multidrug-Resistant Strain Isolated from Sediments of a Polluted River in Mexico, Uncovers New Antibiotic Resistance Genes and a Novel Class-II Lasso Peptide Biosynthesis Gene Cluster

Genome announcements, 2015

Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, g... more Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, generated with PacBio RS II single-molecule real-time technology, consisting of a single circular chromosome of 4.13 Mb. We annotated mobile genetic elements and natural product biosynthesis clusters, including a novel class-II lasso peptide with a 7-residue macrolactam ring.

Research paper thumbnail of Genotypic Characterization ofBradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinti...

Applied and Environmental Microbiology, Jun 1, 1998

We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated... more We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata.

Research paper thumbnail of Complete Genome Sequence of a Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Harboring a Multidrug Resistance IncA/C Plasmid and a blaCMY-2-Carrying IncF Plasmid

Genome announcements, 2015

Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico City,... more Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico City, Mexico, from a patient with a systemic infection, and its complete genome sequence was determined using PacBio single-molecule real-time technology. Strain 33676 harbors an IncF plasmid carrying the extended-spectrum cephalosporin gene blaCMY-2 and a multidrug resistance IncA/C plasmid.

Research paper thumbnail of Genetic and phenotypic analysis of Rhizobium etli and R. tropici mutants defective in lipopolysaccaride synthesis and acid tolerance and applications of genomic typing methods /

Research paper thumbnail of Diversity patterns of Rhizobiaceae communities inhabiting soils, root-surfaces and nodules reveal a strong selection of rhizobial partners by legumes

Environmental microbiology, Jan 23, 2015

Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting o... more Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting our understanding of basic aspects of rhizobial ecology like competitiveness for nodule occupancy and host effects on community structure. We used a combination of cultivation-dependent and independent approaches to analyze alpha and beta diversity patterns of Rhizobiaceae communities from a conserved seasonally-dry tropical forest site in central Mexico and two nearby agricultural fields. Lineage-specific recA amplicon libraries were generated from soil DNA and their sequences compared with those from root-surface and nodule isolates recovered in trapping experiments from two native Acacia species and two Phaseolus vulgaris cultivars. Rarefaction analyses revealed that Rhizobiaceae diversity in soils is larger than on root surfaces, and smallest in nodules. A "rare biosphere"-like distribution of species was found in the three habitats. Multivariate statistical analyses demonst...

Research paper thumbnail of Rhizobial diversity in different land use systems in the rain forest of Los Tuxtlas, Mexico

Research paper thumbnail of Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype

Genome Announcements, 2015

Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the s... more Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids.

Research paper thumbnail of Sustainable Agriculture/Forestry and Biological Nitrogen Fixation

Current Plant Science and Biotechnology in Agriculture, 2005

... Table 4. Rates of symbiotic N2-fixation of some actinorhizal trees and shrubs at field level.... more ... Table 4. Rates of symbiotic N2-fixation of some actinorhizal trees and shrubs at field level. (RO Russo, in D. Werner and WE Newton (eds.) Nitrogen Fixation: Agriculture, Forestry, Ecology and the Environment, Kluwer, 2005) ...

Research paper thumbnail of Análisis evolutivo del virus de la influenza A (H1N1): Un reporte preliminar

Research paper thumbnail of Diversity of Bradyrhizobium Strains Isolated from Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of 16S rDNA and Low-Molecular-Weight Rna Profiles

Current Plant Science and Biotechnology in Agriculture, 2002

Research paper thumbnail of Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes

We present evidence supporting the notion that codon usage (CU) compatibility between foreign gen... more We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient
genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the
fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to
predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU
level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien
genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU
amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete
prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied
additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach
makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing
a novel unbiased framework to study the evolutionary dynamics of HGT.

Research paper thumbnail of Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent, Assessed by Multilocus Sequence Analysis

Applied and …, 2008

A highly supported maximum likelihood species phylogeny for the genus Bradyrhizobium was inferred... more A highly supported maximum likelihood species phylogeny for the genus Bradyrhizobium was inferred from a supermatrix 2 obtained from the concatenation of partial atpD, recA, glnII and rpoB sequences corresponding to 33 reference strains and 3 76 bradyrhizobia isolated from the nodules of Glycine max (soybean) trap plants inoculated with soil samples from 4 Myanmar, India, Nepal and Vietnam. The power of the multigene approach using multiple strains per species was evaluated 5 in terms of overall tree resolution and phylogenetic congruence, representing a practical and portable option for bacterial 6 molecular systematics. Potential pitfalls of the approach are highlighted. Seventy five of the isolates could be classified as 7 B. japonicum type Ia (USDA110/USDA122-like), B. liaoningense, B. yuanmingense or B. elkanii, whereas one represented 8 a novel Bradyrhizobium lineage. Most Nepalese B. japonicum Ia isolates belong to a highly epidemic clone closely related 9 to strain USDA110. Significant phylogenetic evidence was found against the monophyly of the of B. japonicum I and Ia 10 lineages. Analysis of their DNA polymorphisms revealed high population distances, significant genetic differentiation and 11 contrasting population genetic structures, suggesting that the strains in the Ia lineage are misclassified as B. japonicum. The 12 DNA polymorphism patterns of all species conformed to the expectations of the neutral mutation and population 13 equilibrium models and, excluding the B. japonicum Ia lineage, were consistent with intermediate recombination levels. All 14 species displayed epidemic clones and had broad geographic and environmental distribution ranges, as revealed by 15 mapping climate types and geographic origins of the isolates on the species tree. 16 17 A C C E P T E D MATERIALS AND METHODS 1 2 Isolation of symbiotic Bradyrhizobium strains from soybean root nodules. Rhizospheric soil samples were taken from 3 traditionally-managed soybean fields in India, Myanmar, Nepal, and Vietnam without known inoculation records, except for two Indian 4 locations that had been inoculated with B. japonicum . The geographic coordinates, Köppen-Geiger climatic types and 5 agroecological land use of the soil sampling sites are summarized in . The isolates were obtained from the nodules induced by 6 bacteria present in the rhizosphere soil samples on Glycine max trap plants cultivated for 4 weeks using the Leonard jar setting, 7 cultivation conditions and isolation protocols described elsewhere (62). Five gram aliquots of air-dried soil were mixed with the sterile 8 perlite-vermiculite substrate used to fill each cultivation unit. Three jars containing two axenically germinated plantlets were used for 9 each site, whereas jars without soil inoculum served as negative nodulation controls. Genomic DNA from purified isolates and reference 10 strains was isolated using a CTAB-based protocol, as described previously .

Research paper thumbnail of Diversidad genética de bacterias mutualistas de plantas

Research paper thumbnail of Primers4clades: A Web Server to Design Lineage-Specific PCR Primers for Gene-Targeted Metagenomics

Metagenomics and Complementary Approaches, 2011

Research paper thumbnail of Ecolog??a evolutiva de bacterias y el concepto de especie: el caso de los Rizobios

Eguiarte, LE, V. Souza y X. Aguirre (Comps.): …, 2007

... y el concepto de especie: el caso de los rizobios Claudia Silva y Pablo Vinuesa 351 ... Esta ... more ... y el concepto de especie: el caso de los rizobios Claudia Silva y Pablo Vinuesa 351 ... Esta clasificaci??n ubica a la mayor??a de los rizobios en la subclase ?? de las Proteobacterias (Willems y Collins, 1993; Young, 1993; Mart??nez, 1994; Young y Haukka, 1996). ...

Research paper thumbnail of Characterization of Bradyrhizobium SPP. Strains by Rflp analysis of Amplified 16s rDNA and rDNA Intergenic Spacer Regions

Highlights of Nitrogen Fixation Research, 1999

Research paper thumbnail of Identification of a plasmid-borne locus in Rhizobium etli KIM5s involved in lipopolysaccharide O-chain biosynthesis and nodulation of Phaseolus vulgaris

Journal of bacteriology, 1999

Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted ... more Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted in the identification of strain KIM-G1. Its rough colony appearance, flocculation in liquid culture, and Ndv(-) Fix(-) phenotype were indicative of a lipopolysaccharide (LPS) defect. Electrophoretic analysis of cell-associated polysaccharides showed that KIM-G1 produces only rough LPS. Composition analysis of purified LPS oligosaccharides from KIM-G1 indicated that it produces an intact LPS core trisaccharide (alpha-D-GalA-1-->4[alpha-D-GalA-1-->5]-Kdo) and tetrasaccharide (alpha-D-Gal-1-->6[alpha-D-GalA-1-->4]-alpha-D-Man-1-->5Kdo), strongly suggesting that the transposon insertion disrupted a locus involved in O-antigen biosynthesis. Five monosaccharides (Glc, Man, GalA, 3-O-Me-6-deoxytalose, and Kdo) were identified as the components of the repeating O unit of the smooth parent strain, KIM5s. Strain KIM-G1 was complemented with a 7.2-kb DNA fragment from KIM5s that, whe...

Research paper thumbnail of Biocontrol strain Pseudomonas sp. W34: specific detection and quantification in the rhizosphere of Cucumis sativus with a DNA probe and genotypic characterization by DNA fingerprinting

Zeitschrift für Naturforschung. C, Journal of biosciences

A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amp... more A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amplified polymorphic DNA (RAPD) PCR fragments. Specificity of the probe was assessed by dot blot and colony hybridization. It was used to specifically determine the population of these strains on roots of Cucumis sativus cv. Delikatess. Two polymorphic RAPD fragments of 750 bp, and 550 bp showed identical specificity. The biocontrol strain Pseudomonas sp. W34 was shown to be competitive in the rhizosphere of cucumber and to maintain a stable population for at least 10 days when inoculated on the seed. The phylogenetic relationships between the biocontrol and reference strains were analyzed at the strain level by means of RAPD and repetitive sequence-based PCR genomic fingerprinting (rep-PCR), and at higher taxonomic levels by means of amplified 16S ribosomal DNA restriction analysis ARDRA. It was shown that the antagonistic strains are closely related, forming a separate cluster from other...

Research paper thumbnail of Restriction Fragment Length Polymorphism Analysis of 16S rDNA and Low Molecular Weight RNA Profiling of Rhizobial Isolates from Shrubby Legumes Endemic to the Canary Islands

Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic t... more Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic to the Canary islands were characterised by 16S rDNA PCR-RFLP analyses (ARDRA) and LMW RNA profiling, and compared with reference strains representing Bradyrhizobium japonicum, B. elkanii, B. liaoningense, and two unclassified Bradyrhizobium sp. (Lupinus) strains. Both techniques showed similar results, indicating the existence of three genotypes among the Canarian isolates. Analysis of the combined RFLP patterns obtained with four endonucleases, showed the existence of predominant genotype comprising 75% of the Canarian isolates (BTA-1 group) and the Bradyrhizobium sp. (Lupinus) strains. A second genotype was shared by nine Canarian isolates (BGA-1 group) and the B. japonicum and B. liaoningense reference strains. The BES-5 strain formed an independent group, as also did the B. elkanii reference strains. LMW RNA profile analysis consistently resolved the same three genotypes detected by 16S ARDRA among the Canarian isolates, and suggested that all these isolates are genotypically more related to B. japonicum than to B. elkanii or B. liaoningense. Cluster analysis of the combined 16S ARDRA and LMW RNA profiles resolved the BTA-1 group with the Bradyrhizobium sp. (Lupinus) strains, and the BES-5 isolate, as a well separated sub-branch of the B. japonicum cluster. Thus, the two types of analyses indicated that the isolates related to BTA-1 conform a group of bradyrhizobial strains that can be clearly distinguishable from representatives of the tree currently described Bradyrhizobium species. No correlation between genotypes, host legumes, and geographic location was found.

Research paper thumbnail of Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

Front. Microbiol., 2017

The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotro... more The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic

Research paper thumbnail of Complete Genome Sequencing of Stenotrophomonas acidaminiphila ZAC14D2_NAIMI4_2, a Multidrug-Resistant Strain Isolated from Sediments of a Polluted River in Mexico, Uncovers New Antibiotic Resistance Genes and a Novel Class-II Lasso Peptide Biosynthesis Gene Cluster

Genome announcements, 2015

Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, g... more Here, we report the first complete genome sequence of a Stenotrophomonas acidaminiphila strain, generated with PacBio RS II single-molecule real-time technology, consisting of a single circular chromosome of 4.13 Mb. We annotated mobile genetic elements and natural product biosynthesis clusters, including a novel class-II lasso peptide with a 7-residue macrolactam ring.

Research paper thumbnail of Genotypic Characterization ofBradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinti...

Applied and Environmental Microbiology, Jun 1, 1998

We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated... more We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata.

Research paper thumbnail of Complete Genome Sequence of a Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Harboring a Multidrug Resistance IncA/C Plasmid and a blaCMY-2-Carrying IncF Plasmid

Genome announcements, 2015

Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico City,... more Salmonella enterica subsp. enterica serovar Typhimurium strain 33676 was isolated in Mexico City, Mexico, from a patient with a systemic infection, and its complete genome sequence was determined using PacBio single-molecule real-time technology. Strain 33676 harbors an IncF plasmid carrying the extended-spectrum cephalosporin gene blaCMY-2 and a multidrug resistance IncA/C plasmid.

Research paper thumbnail of Genetic and phenotypic analysis of Rhizobium etli and R. tropici mutants defective in lipopolysaccaride synthesis and acid tolerance and applications of genomic typing methods /

Research paper thumbnail of Diversity patterns of Rhizobiaceae communities inhabiting soils, root-surfaces and nodules reveal a strong selection of rhizobial partners by legumes

Environmental microbiology, Jan 23, 2015

Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting o... more Current knowledge about rhizobial diversity patterns in non-nodule habitats is scarce, limiting our understanding of basic aspects of rhizobial ecology like competitiveness for nodule occupancy and host effects on community structure. We used a combination of cultivation-dependent and independent approaches to analyze alpha and beta diversity patterns of Rhizobiaceae communities from a conserved seasonally-dry tropical forest site in central Mexico and two nearby agricultural fields. Lineage-specific recA amplicon libraries were generated from soil DNA and their sequences compared with those from root-surface and nodule isolates recovered in trapping experiments from two native Acacia species and two Phaseolus vulgaris cultivars. Rarefaction analyses revealed that Rhizobiaceae diversity in soils is larger than on root surfaces, and smallest in nodules. A "rare biosphere"-like distribution of species was found in the three habitats. Multivariate statistical analyses demonst...

Research paper thumbnail of Rhizobial diversity in different land use systems in the rain forest of Los Tuxtlas, Mexico

Research paper thumbnail of Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype

Genome Announcements, 2015

Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the s... more Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids.

Research paper thumbnail of Sustainable Agriculture/Forestry and Biological Nitrogen Fixation

Current Plant Science and Biotechnology in Agriculture, 2005

... Table 4. Rates of symbiotic N2-fixation of some actinorhizal trees and shrubs at field level.... more ... Table 4. Rates of symbiotic N2-fixation of some actinorhizal trees and shrubs at field level. (RO Russo, in D. Werner and WE Newton (eds.) Nitrogen Fixation: Agriculture, Forestry, Ecology and the Environment, Kluwer, 2005) ...

Research paper thumbnail of Análisis evolutivo del virus de la influenza A (H1N1): Un reporte preliminar

Research paper thumbnail of Diversity of Bradyrhizobium Strains Isolated from Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of 16S rDNA and Low-Molecular-Weight Rna Profiles

Current Plant Science and Biotechnology in Agriculture, 2002

Research paper thumbnail of Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes

We present evidence supporting the notion that codon usage (CU) compatibility between foreign gen... more We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient
genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the
fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to
predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU
level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien
genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU
amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete
prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied
additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach
makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing
a novel unbiased framework to study the evolutionary dynamics of HGT.

Research paper thumbnail of Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent, Assessed by Multilocus Sequence Analysis

Applied and …, 2008

A highly supported maximum likelihood species phylogeny for the genus Bradyrhizobium was inferred... more A highly supported maximum likelihood species phylogeny for the genus Bradyrhizobium was inferred from a supermatrix 2 obtained from the concatenation of partial atpD, recA, glnII and rpoB sequences corresponding to 33 reference strains and 3 76 bradyrhizobia isolated from the nodules of Glycine max (soybean) trap plants inoculated with soil samples from 4 Myanmar, India, Nepal and Vietnam. The power of the multigene approach using multiple strains per species was evaluated 5 in terms of overall tree resolution and phylogenetic congruence, representing a practical and portable option for bacterial 6 molecular systematics. Potential pitfalls of the approach are highlighted. Seventy five of the isolates could be classified as 7 B. japonicum type Ia (USDA110/USDA122-like), B. liaoningense, B. yuanmingense or B. elkanii, whereas one represented 8 a novel Bradyrhizobium lineage. Most Nepalese B. japonicum Ia isolates belong to a highly epidemic clone closely related 9 to strain USDA110. Significant phylogenetic evidence was found against the monophyly of the of B. japonicum I and Ia 10 lineages. Analysis of their DNA polymorphisms revealed high population distances, significant genetic differentiation and 11 contrasting population genetic structures, suggesting that the strains in the Ia lineage are misclassified as B. japonicum. The 12 DNA polymorphism patterns of all species conformed to the expectations of the neutral mutation and population 13 equilibrium models and, excluding the B. japonicum Ia lineage, were consistent with intermediate recombination levels. All 14 species displayed epidemic clones and had broad geographic and environmental distribution ranges, as revealed by 15 mapping climate types and geographic origins of the isolates on the species tree. 16 17 A C C E P T E D MATERIALS AND METHODS 1 2 Isolation of symbiotic Bradyrhizobium strains from soybean root nodules. Rhizospheric soil samples were taken from 3 traditionally-managed soybean fields in India, Myanmar, Nepal, and Vietnam without known inoculation records, except for two Indian 4 locations that had been inoculated with B. japonicum . The geographic coordinates, Köppen-Geiger climatic types and 5 agroecological land use of the soil sampling sites are summarized in . The isolates were obtained from the nodules induced by 6 bacteria present in the rhizosphere soil samples on Glycine max trap plants cultivated for 4 weeks using the Leonard jar setting, 7 cultivation conditions and isolation protocols described elsewhere (62). Five gram aliquots of air-dried soil were mixed with the sterile 8 perlite-vermiculite substrate used to fill each cultivation unit. Three jars containing two axenically germinated plantlets were used for 9 each site, whereas jars without soil inoculum served as negative nodulation controls. Genomic DNA from purified isolates and reference 10 strains was isolated using a CTAB-based protocol, as described previously .

Research paper thumbnail of Diversidad genética de bacterias mutualistas de plantas

Research paper thumbnail of Primers4clades: A Web Server to Design Lineage-Specific PCR Primers for Gene-Targeted Metagenomics

Metagenomics and Complementary Approaches, 2011

Research paper thumbnail of Ecolog??a evolutiva de bacterias y el concepto de especie: el caso de los Rizobios

Eguiarte, LE, V. Souza y X. Aguirre (Comps.): …, 2007

... y el concepto de especie: el caso de los rizobios Claudia Silva y Pablo Vinuesa 351 ... Esta ... more ... y el concepto de especie: el caso de los rizobios Claudia Silva y Pablo Vinuesa 351 ... Esta clasificaci??n ubica a la mayor??a de los rizobios en la subclase ?? de las Proteobacterias (Willems y Collins, 1993; Young, 1993; Mart??nez, 1994; Young y Haukka, 1996). ...

Research paper thumbnail of Characterization of Bradyrhizobium SPP. Strains by Rflp analysis of Amplified 16s rDNA and rDNA Intergenic Spacer Regions

Highlights of Nitrogen Fixation Research, 1999

Research paper thumbnail of Identification of a plasmid-borne locus in Rhizobium etli KIM5s involved in lipopolysaccharide O-chain biosynthesis and nodulation of Phaseolus vulgaris

Journal of bacteriology, 1999

Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted ... more Screening of derivatives of Rhizobium etli KIM5s randomly mutagenized with mTn5SSgusA30 resulted in the identification of strain KIM-G1. Its rough colony appearance, flocculation in liquid culture, and Ndv(-) Fix(-) phenotype were indicative of a lipopolysaccharide (LPS) defect. Electrophoretic analysis of cell-associated polysaccharides showed that KIM-G1 produces only rough LPS. Composition analysis of purified LPS oligosaccharides from KIM-G1 indicated that it produces an intact LPS core trisaccharide (alpha-D-GalA-1-->4[alpha-D-GalA-1-->5]-Kdo) and tetrasaccharide (alpha-D-Gal-1-->6[alpha-D-GalA-1-->4]-alpha-D-Man-1-->5Kdo), strongly suggesting that the transposon insertion disrupted a locus involved in O-antigen biosynthesis. Five monosaccharides (Glc, Man, GalA, 3-O-Me-6-deoxytalose, and Kdo) were identified as the components of the repeating O unit of the smooth parent strain, KIM5s. Strain KIM-G1 was complemented with a 7.2-kb DNA fragment from KIM5s that, whe...

Research paper thumbnail of Biocontrol strain Pseudomonas sp. W34: specific detection and quantification in the rhizosphere of Cucumis sativus with a DNA probe and genotypic characterization by DNA fingerprinting

Zeitschrift für Naturforschung. C, Journal of biosciences

A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amp... more A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amplified polymorphic DNA (RAPD) PCR fragments. Specificity of the probe was assessed by dot blot and colony hybridization. It was used to specifically determine the population of these strains on roots of Cucumis sativus cv. Delikatess. Two polymorphic RAPD fragments of 750 bp, and 550 bp showed identical specificity. The biocontrol strain Pseudomonas sp. W34 was shown to be competitive in the rhizosphere of cucumber and to maintain a stable population for at least 10 days when inoculated on the seed. The phylogenetic relationships between the biocontrol and reference strains were analyzed at the strain level by means of RAPD and repetitive sequence-based PCR genomic fingerprinting (rep-PCR), and at higher taxonomic levels by means of amplified 16S ribosomal DNA restriction analysis ARDRA. It was shown that the antagonistic strains are closely related, forming a separate cluster from other...

Research paper thumbnail of Restriction Fragment Length Polymorphism Analysis of 16S rDNA and Low Molecular Weight RNA Profiling of Rhizobial Isolates from Shrubby Legumes Endemic to the Canary Islands

Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic t... more Thirty-six strains of slow-growing rhizobia isolated from nodules of four woody legumes endemic to the Canary islands were characterised by 16S rDNA PCR-RFLP analyses (ARDRA) and LMW RNA profiling, and compared with reference strains representing Bradyrhizobium japonicum, B. elkanii, B. liaoningense, and two unclassified Bradyrhizobium sp. (Lupinus) strains. Both techniques showed similar results, indicating the existence of three genotypes among the Canarian isolates. Analysis of the combined RFLP patterns obtained with four endonucleases, showed the existence of predominant genotype comprising 75% of the Canarian isolates (BTA-1 group) and the Bradyrhizobium sp. (Lupinus) strains. A second genotype was shared by nine Canarian isolates (BGA-1 group) and the B. japonicum and B. liaoningense reference strains. The BES-5 strain formed an independent group, as also did the B. elkanii reference strains. LMW RNA profile analysis consistently resolved the same three genotypes detected by 16S ARDRA among the Canarian isolates, and suggested that all these isolates are genotypically more related to B. japonicum than to B. elkanii or B. liaoningense. Cluster analysis of the combined 16S ARDRA and LMW RNA profiles resolved the BTA-1 group with the Bradyrhizobium sp. (Lupinus) strains, and the BES-5 isolate, as a well separated sub-branch of the B. japonicum cluster. Thus, the two types of analyses indicated that the isolates related to BTA-1 conform a group of bradyrhizobial strains that can be clearly distinguishable from representatives of the tree currently described Bradyrhizobium species. No correlation between genotypes, host legumes, and geographic location was found.