Víctor González

• National Autonomous University of Mexico

This study aimed to investigate the impact of various common beans (Phaseolus vulgaris L.) cultivars on the bacterial communities in the rhizosphere under local agricultural conditions. Even though the differences in cultivation history and physicochemical properties of nearby agriculture plots, the bacterial community in the bulk soil was quite si...

The rhizosphere of crop plants is a nutrient-rich niche that is inhabited by many microorganisms. Root-associated microorganisms play a crucial role in crop yields in agriculture. Given the ample diversity of varieties and cultivars of the common bean ( Phaseolus vulgaris ) used in agriculture, it is important to characterize their bacterial commun...

This study describes novel single-stranded DNA phages isolated from common bean agriculture soils by infection of the nitrogen-fixing symbiotic bacteria Rhizobium etli and R. phaseoli. A total of 29 phages analyzed have 4.3–6 kb genomes in size and GC 59–60%. They belong to different clades unrelated to other Microviridae subfamilies. Three-dimensi...

In this study, we addressed the extent of diversification of phages associated with nitrogen-fixing symbiotic Rhizobium species. Despite the ecological and economic importance of the Rhizobium genus, little is known about the diversity of the associated phages. A thorough assessment of viral diversity requires investigating both lytic phages and pr...

A Correction to this paper has been published: https://doi.org/10.1038/s41396-021-00963-5

Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, known as rhizobia, have been shown to locally ad...

Bacillus velezensis 83 was isolated from mango tree phyllosphere of orchards located in El Rosario, Sinaloa, México. The assessment of this strain as BCA (biological control agent), as well as PGPB (plant growth-promoting bacteria), were demonstrated through in vivo and in vitro assays. In vivo assays showed that B. velezensis 83 was able to contro...

Bacteriophages play significant roles in the composition, diversity, and evolution of bacterial communities. Despite their importance, it remains unclear how phage diversity and phage-host interactions are spatially structured. Local adaptation may play a key role. Nitrogen-fixing symbiotic bacteria, called rhizobia, have been shown to locally adap...

Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroq...

Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study. Resistance to methicillin, beta-lactams, fluoroquinolones, a...

The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain the...

Comparison of the complete proteomes of the symbiotic plasmids of R. leguminosarum. Unidirectional BLASTp using the total predicted proteins of R. leguminosarum 3841 pRL10 symbiotic plasmid (illustrated by the red innermost circle) against the predicted proteins of others symbiotic plasmid indicated in the inset. Blast hits were recorded and showed...

Correlation between ANIm and Gcov. (a) 102 Rhizobium and Sinorhizobium genomes, (b) 88 genomes, (c) 35 genomes of rC-I clade, and (d) 38 genomes o rC-II clade. Spearman r and p-values are indicated in the inset.

Distribution of ANI values between pairs of genomes belonging to (a) 102 genomes, (b) 88 genomes, (c) and (e) 35 genomes of rC-I clade, and (d) and (f) 38 genomes o rC-II clade. Histograms show the frequency of pairwise comparisons within clades (turquoise color), and inter clades (pale red), distributed by segments of ANI values. In figures (e) an...

The collection of genomes of Rhizobium and Sinorhizobium used in this study.

Phylogenetic tree of ribosomal proteins of Rhizobium species. Ribosomal clades are indicated by Roman numerals (I to VI) enclosed in colored ellipses. Subclades appear with black ellipses within the clades. The tree was constructed using maximum likelihood in the MEGA software package, by using 58 concatenated ribosomal proteins (refer to section “...

Genomic clusters of 102 Rhizobium and Sinorhizobium pairs obtained by pairwise ANIm comparisons.

Correlation between ANIm and ANIb in pairwise comparison of 102 Rhizobium and Sinorhizobium genomes. Spearman r and p-values are shown.

Phylogenetic families of RepB. Phylogenies were constructed with the maximum likelihood method and a bootstrap of n = 1000 replicates. Colors indicate the phylogenetic clades and their correspondence with the MCL clusters determined as indicated in the section “Materials and Methods” and Figure 5.

Correlation between Gcov and phylogenetic distance. (a) 102 Rhizobium and Sinorhizobium genomes, (b) 88 genomes, (c) 35 genomes of rC-I clade, and (d) 38 genomes o rC-II clade. Spearman r and p-values are shown.

Pairwise ANIm comparison between complete R. leguminosarum symbiotic plasmids. Only the genome sequences of R. leguminosarum listed in the GenBank up to 14-03-2019 were downloaded. The ANIm comparison were performed using JSspecies as described in the methods section. The heatmap show the values of the corrected Gcov% / ANIm%; the color scale key i...

Bray Curtis dissimilarity index for accessory genes distribution within and between ribosomal clusters.

Staphylococcus epidermidis is a human commensal and opportunistic pathogen worldwide distributed. To ascertain which pathogenic S. epidermidis clones are circulating in a local tertiary hospital setting, we sequenced the complete genomes of 17 S. epidermidis isolates obtained from neonatal infections at a Hospital Care Unit in México City. Genomic...

Staphylococcus epidermidis is a human commensal and opportunistic pathogen worldwide distributed. To ascertain which pathogenic S. epidermidis clones are circulating in a local tertiary hospital setting, we sequenced the complete genomes of 17 S. epidermidis isolates obtained from neonatal infections at a Hospital Care Unit in México City. Genomic...

We present here the high-quality complete genome sequences of eight strains of Rhizobium -nodulating Phaseolus vulgaris . Comparative analyses showed that some of them belonged to different genomic and evolutionary lineages with common symbiotic properties. Two novel symbiotic plasmids (pSyms) with P. vulgaris specificity are reported here.

An Acinetobacter strain, designated ACE, was isolated in the laboratory. Phylogenetic tests and average nucleotide identity value comparisons suggested that ACE belongs to the species Acinetobacterschindleri. We report for the first time the complete genome sequence of an A. schindleri strain, which consists of a single circular chromosome of 3 001...

The whole-genome sequences of three strains of Rhizobium gallicum reported here support the concept that the distinct nodulation host ranges displayed by the symbiovars gallicum and phaseoli can be largely explained by different symbiotic plasmids.

Cultivated common beans are the primary protein source for millions of people around the world who subsist on low-input agriculture, enabled by the symbiotic N2 -fixation these legumes perform in association with rhizobia. Within a single agricultural plot, multiple Rhizobium species can nodulate bean roots, but it is unclear how genetically isolat...

RESUMEN. Se colectaron garrapatas de Rhipicephalus (Boophilus) microplus durante los años 2010 a 2015 de bovinos infestados experimentalmente. Estas garrapatas mostraron signos de infección natural, como la presencia de exudado en el hipostoma y poro genital, cambio de coloración de la cutícula y bloqueo en la oviposición de hembras ingurgitadas qu...

Aeromonas caviae is an emerging human pathogen. Here, we report the draft genome sequence of Aeromonas caviae strain 429865 INP which shows the presence of various putative virulence-related genes.

Bioinformatics tools are essential for extracting valuable biological knowledge from bacterial genomes. Currently, there are many computational applications, algorithms, and programs to decipher the genomes in terms of structure, function, and evolution. Specialized databases to upload and retrieve genomic information have grown as well in the last...

Background Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodu...

In this work, we isolated and characterized 14 bacteriophages that infect Rhizobium etli. They were obtained from rhizosphere soil of bean plants from agricultural lands in Mexico using an enrichment method. The host range of these phages was narrow but variable within a collection of 48 R. etli strains. We obtained the complete genome sequence of...

Tapeworms (Cestoda) cause neglected diseases that can be fatal and are difficult to treat, owing to inefficient drugs. Here we present an analysis of tapeworm genome sequences using the human-infective species Echinococcus multilocularis, E. granulosus, Taenia solium and the laboratory model Hymenolepis microstoma as examples. The 115- to 141-megab...

Sinorhizobium fredii GR64 is a peculiar strain that is able to effectively nodulate bean but not soybean, the common host of S. fredii. Here we present the draft genome of S. fredii GR64. This information will contribute to a better understanding of the symbiotic rhizobium-plant interaction and of rhizobial evolution.

Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an addi...

Here we present the genome sequence of Rhizobium grahamii CCGE502. R. grahamii groups with other newly described broad-host-range species, which are not very efficient Phaseolus vulgaris symbionts, with a wide geographic distribution and which constitutes a novel Rhizobium clade.

In this work, Escherichia coli MG1655 was engineered to produce ethanol and evolved in a laboratory process to obtain an acetate tolerant strain called MS04 (E. coli MG1655: ΔpflB, ΔadhE, ΔfrdA, ΔxylFGH, ΔldhA, PpflB::pdc Zm -adhB Zm , evolved). The growth and ethanol production kinetics of strain MS04 were determined in mineral medium, mainly unde...

Although bacteria of the genus Wolbachia induced significant extended phenotypes to infected hosts, most molecular mechanisms involved are still unknown. To gain insight into the bacterial genetic determinants, we sequenced the whole genome of Wolbachia wAlbB strain, a commensal obligate intracellular of the tiger mosquito Aedes albopictus.

Chemotaxis operons in Azospirillum. F5, F9 and ACF class chemotaxis systems were present in a common ancestor of azospirilla and other Rhodospirillaceae (e.g. Rhodospirillum centenum) [65], [66]. The F7 system was horizontally transferred to a common ancestor of Azospirillum. The F8 system was horizontally transferred to a common ancestor of Azospi...

Typical habitats of Rhodospirillaceae. (PDF)

Genes that are potentially involved in adaptation of Azospirillum to the rhizosphere and its interaction with host plants. (PDF)

Orthologous chemotaxis operons in Azospirillum and Rhodospirillum centenum. (PDF)

Abundance of the F7 chemotaxis system in the rhizosphere. Chemotaxis systems were assigned as described in SI Materials and Methods. See Table S11 for detailed information. (TIF)

Chromosomes, chromids, and plasmids in Azospirillum genomes. Schematic representation of chromosomes, chromids and plasmids of A. lipoferum 4B (A to G) and A. brasilense Sp245 (H to N). Radii are not to scale. The two outer rings (1 and 2) represent genes on the forward and reverse strands, respectively, colored by COG functional categories: red, I...

Origin of Azospirillum genes. (PDF)

Divergence in the 16S rRNA gene between Azospirillum lipoferum 4B and other members of Rhodospirillaceae. (PDF)

Proteomic analysis of Azospirillum. (PDF)

Classification of chemotaxis systems in rhizosphere. (PDF)

Identification of chromids in Azospirillum by house-keeping gene analysis. (PDF)

Identification of chromids in Azospirillum by GC content. (PDF)

ANI analysis of Azospirillum and rhizobial genomes. (PDF)

Recombination hotspots in Azospirillum genomes. (PDF)

Putative complex carbohydrate-degrading enzymes in three Azospirillum species in comparison with a soil cellulolytic bacterium Thermobifida fusca. (PDF)

Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; howev...

Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria Rhizobium etli is highly variable in both genomic structure and gene content. However, no prev...

Strategy for Determining SNPs. The additional file (in .pdf format) includes text and figures delineating our process for determining SNPs (parameters, paired comparisons and SNP differences). Also include the distribution of functional classes (COGs) of recombinant quartets of each draft genome and your comparison against distribution of CFN42.

Table of genes presented in 240 shared regions. The additional file (in .xls) includes the tables of genes and your features, as name, coordinates, gi, COGs and other.

Strains of the same bacterial species often show considerable genomic variation. To examine the extent of such variation in Rhizobium etli, the complete genome sequence of R. etli CIAT652 and the partial genomic sequences of six additional R. etli strains having different geographical origins were determined. The sequences were compared with each o...

Insertion sequences (IS) are mobile genetic elements that are distributed in many prokaryotes. In particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, IS are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. Here, we report an analysis of the distribution an...

Abbreviations of additional file 3. Abbreviations used in the pairwise identity plots in additional file 3.

Robison-Fould distances between Rep phylogenies. In order to determine the similarity among the Rep phylogenies, Robison-Fould distances between Rep phylogenies were established.

Functional restrictions within RepC. Substitution rate variation among sites in RepC. All sites were assigned to one of five gamma categories. Pfam-A domains are shown, as well as the zone affected by recombination events.

Genomes used. Alphaproteobacteria genomes used to search for repABC operons.

Homologous genes and repABC operons. Homologous genes of repA, repB, and repC, as well as complete and faulty repABC operons found across the studied Alphaproteobacteria genomes. For each gene it was registered whether it was located on a chromosome (C) or a plasmid (P).

Recombination events identified for repA, repB, and repC. Pairwise identity plots of the localized recombination events, showing major and minor parent sequences as well as the daughter sequence. Abbreviations are given in Additional file 4.

The repABC plasmid family, which is extensively present within Alphaproteobacteria, and some secondary chromosomes of the Rhizobiales have the particular feature that all the elements involved in replication and partitioning reside within one transcriptional unit, the repABC operon. Given the functional interactions among the elements of the repABC...

The presence of bla(SHV-5) is described in a compound transposon, duplicated in tandem and flanked by IS26 copies on a 70-kb conjugative plasmid (pHNM1), in an Enterobacter cloacae strain associated with a nosocomial outbreak that occurred in Mexico.

The physiological role and transcriptional expression of Rhizobium etli sigma factors rpoH1 and rpoH2 are reported in this work. Both rpoH1 and rpoH2 were able to complement the temperature-sensitive phenotype of an Escherichia coli rpoH mutant. The R. etli rpoH1 mutant was sensitive to heat shock, sodium hypochlorite and hydrogen peroxide, whereas...

En el contexto del proyecto MiZona , se utiliza la Competencia Instrumental Uso de TICs, en el tiempo libre del estudiante, para reforzar a través de su apropiación indirecta, esta competencia genérica. El estudio esta basado en un diseño cuasi – experimental en el cual el grupo de intervención son los alumnos de primer año de la Carrera Plan Comú...

As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual p...

General features of the Genomes of R.etli and R.leguminosarum. A comparison of the main features of the genomes of Rhizobium leguminosarum and Rhizobium etli. Each replicon is described in terms of length in base pairs, %G+C content and number of coding sequences (CDS). (0.04 MB DOC)

Phylogenetic tree. Maximum likelihood phylogenetic tree showing bacteria related to R.etli and R.leguminosarum (0.08 MB TIF)

Chimeric structure of R.etli plasmid p42d. The circles show (outermost to innermost): 1. Atypical regions as bars of degraded colour (red to pale rose) according to the scores obtained from Alien Hunter (red, highest score 73 over a threshold of 32). 2. The 125 kb nif-nod region. 3, CDS of p42d according to the following colour code: blue, nodulati...

[This corrects the article on p. e2567 in vol. 3, PMID: 18596979.].

This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly s...

This paper demonstrates experimentally the viabilit y of the wireless technology IEEE 802.11b for inter-vehicle communications. Although IEEE802.11b was designed for low- mobility, indoor scenarios, we demonstrate that is possible to use it in high-mobility, outdoor scenarios where ve hicles reach relative speeds of 260 km/h. For the first time, th...

Symbiotic bacteria, known as rhizobia, interact with the roots of leguminous plants and develop nitrogen-fixing nodules. In this chapter, we will focus on the comparison of the complete genomes of Mesorhizobium loti, Sinorhizobium meliloti, Bradyrhizobium japonicum, Rhizobium leguminosarum, and Rhizobium etli. These bacteria contain the symbiosis g...

The prevalence of bacteriophages was investigated in 24 strains of four species of plant growth-promoting rhizobacteria belonging to the genus Azospirillum. Upon induction by mitomycin C, the release of phage particles was observed in 11 strains from three species. Transmission electron microscopy revealed two distinct sizes of particles, depending...

Several lines of evidence suggest that reiterated sequences in the human genome are targets for nonallelic homologous recombination (NAHR), which facilitates genomic rearrangements. We have used a PCR-based approach to identify breakpoint regions of rearranged structures in the human genome. In particular, we have identified intrachromosomal identi...

Fabaceae (legumes) is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes) for these crops is limited. We sequenced the complete genome of the common bean (...

The comparative analysis of genomic characteristics and single-nucleotide polymorphism patterns from large fragments borne on different replicons of Sinorhizobium spp. genomes clearly demonstrate that DNA recombination among closely related bacteria is a major event in the diversification of this genome, especially in pSymA, resulting in mosaic str...

While most mammals including the prosimians have a single copy of the growth hormone (GH) gene, anthropoids possess a cluster of GH-related genes. Throughout the evolution of the main anthropoid groups [New World Monkeys (NWM), Old World Monkeys (OWM), and apes], two features stand out of the GH loci. The first is the appearance of chorionic somato...

We report the complete 6,530,228-bp genome sequence of the symbiotic nitrogen fixing bacterium Rhizobium etli. Six large plasmids comprise one-third of the total genome size. The chromosome encodes most functions necessary for cell growth, whereas few essential genes or complete metabolic pathways are located in plasmids. Chromosomal synteny is dis...

A collection of Rhizobium etli promoters was isolated from a genomic DNA library constructed in the promoter-trap vector pBBMCS53, by their ability to drive the expression of a gusA reporter gene. Thirty-seven clones were selected, and their transcriptional start-sites were determined. The upstream sequence of these 37 start-sites, and the sequence...