Genomic characterization of multidrug-resistant extraintestinal pathogenic Escherichia coli isolated from grain culture soils

Multidrug-resistant (MDR) Escherichia coli, mainly extraintestinal pathogenic E. coli (ExPEC), has been widely reported in infections worldwide. In agricultural soils, manure is a hotspot for the dissemination of antimicrobial resistance genes (ARGs) and pathogenic bacteria; however, MDR bacteria have also been reported in soils with no history of manure use. In addition, cross-resistance and co-resistance have been described as responsible for the metal-driven selection of bacteria resistant to antimicrobials. Therefore, the aim of this study was to analyze three MDR E. coli isolates obtained from Brazilian grain culture soil samples with no history of manure use by whole-genome sequencing. The MDR E. coli isolates were recovered from soils from corn and coffee fields, and presented resistance to β-lactams, quinolones, aminoglycosides, tetracyclines, sulphonamides, and dihydrofolate reductase inhibitor. Resistome analysis showed ARGs to several antimicrobials (i.e., β-lactams, tetracyclines, aminoglycosides, sulphonamides, trimethoprim, phenicols, fosfomycin, and macrolides) as well as several metal resistance genes and antibacterial biocide resistance genes. In addition, known mutations in quinolone-resistance-determining regions of GyrA (Ser83Leu and Asp87Asn), ParE (Ser458Thr), and ParC (Ser80Ile) were also detected. Virulome analysis showed the presence of virulence genes (lpfA, mcmA, gad, mchF, iroN, cma, and iss) associated with ExPEC. Multidrug-resistant ExPEC isolates were assigned to phylogenetic group B1. The presence of MDR B1-ExPEC in soil samples shows the ability of these isolates to survive in soils. This study reports for the first time some sequence types (i.e., ST345, ST448, and ST1146) of MDR E. coli in Brazilian soils. Therefore, these findings contribute to the monitoring of antimicrobial resistance and surveillance studies based on whole-genome sequencing worldwide.     

Reservoir sediment characterisation by diffuse reflectance spectroscopy in a semiarid region to support sediment reuse for soil fertilization

Journal of Soils and Sediments - Soil erosion by water yields sediment to surface reservoirs, reducing their storage capacities, changing their geometry, and degrading water quality. Sediment...     

Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond,and its relationships with agronomic traits

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and molecular characterization. Our objectives were to: estimate genetic similarities (GS), marker indices, and polymorphic information contents (PICs) for AFLP markers in almond cultivars; assess the genetic diversity of almond cultivars and wild species, using GS estimated from AFLP fingerprints and molecular characterization; and facilitate the use of markers in inter-specific introgression and cultivar improvement. The genetic diversity of 45 almond cultivars from Iran, Europe, and America, were studied assaying 19 primer combinations. In addition, several agronomic traits were evaluated, including flowering and maturity times, self-incompatibility, and kernel and fruit properties. Out of the 813 polymerase chain reaction fragments that were scored, 781 (96.23%) were polymorphic. GS ranged from 0.5 to 0.96, marker indices ranged from 51.37 to 78.79, and PICs ranged from 0.56 to 0.86. Results allowed the unique molecular identification of all assayed genotypes. However, the correlation between genetic similarity clustering as based on AFLP and clustering for agronomic traits was low. Cluster analysis based on AFLP data clearly differentiated the genotypes and wild species according to their origin and pedigree, whereas, cluster analysis based on agronomic data differentiated according the pomological characterization. Our results showed the great genetic diversity of the almond cultivars and their interest for almond breeding.     

Responses to water withdrawal of tobacco plants genetically engineered with the AtTPS1 gene: a special reference to photosynthetic parameters

We have previously obtained several lines of tobacco transformed with a trehalose-6-phosphate synthase gene of plant origin (Arabidopsis thaliana), involved in the first step of the biosynthesis of trehalose, a known osmoprotectant. Two showed distinct intensity of expression: high (B5H) and low (B1F). Such lines were analyzed for trehalose-6-phosphate content and the obtained results demonstrated to be in accordance with the expression results. In order to study the responses of photosynthesis to water deficit of transgenic lines in comparison to wild type (WT), three experiments were performed under different conditions: (1) Relative water (2) Leaf gas exchange (3) Modulated Chlorophyll a Fluorescence. Different responses in RWC of plant lines to water withdrawal were detected, with transgenic line B5H indicating less water loss after the water withdrawal period. Similar responses to water deficit regarding the leaf gas exchanges were recorded for the three lines. When subjected to water deficit stress situations, higher F _v/F _m, Φ_PSII and qP were detected for the transgenic lines. Under a SWC of 20% where higher values for such parameters were detected with special relevance for the B5H line, indicating a possible higher ability to withstand severe drought stress and to resist to prolonged periods without water than the B1F and WT lines.     

Genetic variability measures among Bromus catharticus Vahl. populations and cultivars with RAPD and AFLP markers

The objectives of this study were to optimize RAPD and AFLP techniques in B. catharticus, and to determine the genetic variability of populations and commercial prairie grass cultivars with the aforementioned molecular markers. Two populations with contrasting morphological characteristics were evaluated from individual and bulked DNA samples using RAPD markers. Both analyses showed a similar information about inter population variability. Each accession was sampled by a single leaf bulk of 10 plants. Accession similarities were established with 276 RAPD and 714 AFLP bands using Jaccard similarity coefficient. The dendrogram of the accessions using RAPD markers showed that they shared high similarity values (>94%). A similar result was obtained with AFLP markers (similarity values >98%), revealing a narrow genetic basis in the analyzed accessions. Consequently, molecular characterization of germplasm should be considered in addition to morphological criteria, to choose the parental genotypes for breeding programs of this forage crop. The AFLP technique was more efficient to detect DNA polymorphism in our experiments and unique fingerprints were detected for all the accessions. RAPD is a simple and non expensive technique, suitable to estimate genetic similarity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Inheritance and relationships of important agronomic traits in almond

The inheritance of 16 important agronomic traits and its relationship were studied for four years in a population of 167 almond [P. dulcis (Mill.) D.A. Webb] seedlings obtained from a cross between the French selection ‘R1000’ (‘Tardy Nonpareil’ × ‘Tuono’) and the Spanish cultivar ‘Desmayo Largueta’. For some traits (blooming and leafing date) descendants segregated between the value of both progenitors, meanwhile for others the mean of the offspring was lower (bloom density, productivity and ripening date) or higher (in-shell/kernel ratio and double kernels). As expected, kernel bitterness and self-incompatibility behaved as monogenic traits. Some important correlations between traits were detected. The implications of the transmission and the correlation of these traits in the breeding programmes are discussed.     

A male-fertile Lycopersicon esculentum × Solanum lycopersicoides hybrid enables direct backcrossing to tomato at the diploid level

Solanum lycopersicoides Dun. is a wild nightshade native to Chile and Peru that possesses many traits of potential interest to tomato breeders, including environmental stress tolerance, resistances to disease and insect pests, and certain fruit quality characteristics. Sexual and somatic hybrids with the cultivated tomato (Lycopersicon esculentum Mill.) are readily obtained, yet have a strong tendency towards male-sterility combined with unilateral incompatibility, barriers that have deterred breeding efforts in the past. We report herein the synthesis of a partially male-fertile F₁ hybrid by sexual crosses between tomato and a recently collected population of S. lycopersicoides. Over 280 BC₁ plants were obtained by directed backcrossing to tomato at the diploid level, of which 58 were sufficiently fertile to permit selfing or additional backcrosses. The transmission of S. lycopersicoides genetic markers into a uniform L. esculentum background was confirmed with 24 isozyme or morphological loci on 11 of the 12 alien chromosomes. Potentially useful tolerance to gray mold (Botrytis cinerea) was demonstrated by inoculation of stem cuttings with mycelial plugs: at 6 days post-inoculation, the intergeneric hybrid showed little evidence of disease progression and the length of stem lesions averaged only one third that of susceptible controls. This revised version was published online in July 2006 with corrections to the Cover Date.     

Structuring of some basic pedological processes

In the first section, the author presents a detailed analysis of fundamental processes of pedological evolution in the light of the latest findings as to biogeochemical, mineralogical and granulometric aspects of pedogenesis on crystalline aluminosilicate rocks. This analysis is based on the nature of various geochemical weathering phenomena, on the one hand, and on problems related to the organization of plasmic elements (pédoplasmation) and their possible transfers as particles, on the other. With reference to the latter aspect, two major types of “pedogenesis” may be considered: “associative” pedogenesis in which plasma-skeleton links are kept, and “dissociative” pedogenesis in which plasma—skeleton links are disrupted and plasma is redistributed.Then, in the second section, a structuring of fundamental pedogenetic processes is proposed, based on the observation of three major phyla at the earth surface.Phylum I: Process with predominant biogeochemical evolution without plasma formation or with plasma destruction.Phylum II: Process with predominant biogeochemical evolution with plasma formation and reorganization in situ.Phylum III: Process with predominant textural evolution with plasma mobilization and redistribution.