Search results for "Microbial"
showing 10 items of 2041 documents
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics
2017
Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results f…
Evolution of organic carbon pools and microbial diversity in hyperarid anthropogenic soils
2016
Abstract We investigated the organic carbon pools and the microbial diversity and activity in anthropogenic terraced soils in a desert area of Southern Peru to highlight how the introduction of agriculture influences carbon evolution and storage and genetic and functional diversity of soil microbiota over time. Five sites were selected considering soils cultivated since 5, 15, 20, 35 and 65 years, sampled along the profile depth (0–20 and 20–40 cm layer). Soil and microbial parameters comprised by organic carbon pools, microbial respiration, microbial community physiological profile (CLPP) and microbial diversity (PCR-DGGE) were determined. The results showed that the highest C concentratio…
Distribution, redox state and (bio)geochemical implications of arsenic in present day microbialites of Laguna Brava, Salar de Atacama
2018
Understanding how microorganisms adapted to the high arsenic concentration present on early Earth requires understanding of the processes involved in the arsenic biogeochemical cycle operating in living microbial mats. To this end, we investigated a living microbial mat from Laguna Brava (Salar de Atacama, Chile), a hypersaline lake with high arsenic concentration, using an array of conventional geochemical techniques, such as X-ray diffraction, SEM-EDX and Confocal Laser Scanning Microscopy (CLSM), combined with state-of-the-art high resolution scanning imaging techniques, including X-ray micro-fluorescence (μXRF) and X-ray Absorption Near Edge Structure (XANES) mapping. This experimental …
Resistant ammonia-oxidizing archaea endure, but adapting ammonia-oxidizing bacteria thrive in boreal lake sediments receiving nutrient-rich effluents
2018
Climate change along with anthropogenic activities changes biogeochemical conditions in lake ecosystems, modifying the sediment microbial communities. Wastewater effluents introduce nutrients and organic material but also novel microbes to lake ecosystems, simulating forthcoming increases in catchment loadings. In this work, we first used 16s rRNA gene sequencing to study how the overall sediment microbial community responds to wastewater in six boreal lakes. To examine forthcoming changes in the lake biogeochemistry, we focused on the ammonia-oxidizing archaea (AOA) and bacteria (AOB), and examined their functional and compositional community response to wastewater. Although we found the l…
Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics
2016
Bacteria of the genus Pseudomonas occupy diverse environments. The Pseudomonas fluorescens group is particularly well-known for its plant-beneficial properties including pathogen suppression. Recent observations that some strains of this group also cause lethal infections in insect larvae, however, point to a more versatile ecology of these bacteria. We show that 26 P. fluorescens group strains, isolated from three continents and covering three phylogenetically distinct sub-clades, exhibited different activities toward lepidopteran larvae, ranging from lethal to avirulent. All strains of sub-clade 1, which includes Pseudomonas chlororaphis and Pseudomonas protegens, were highly insecticidal…
Resistance profiles and risk factors of resistant microorganisms in bacteraemia of abdominal origin
2017
Abstract Objective The presence of resistant microorganisms is a major cause of failure in initial empirical antimicrobial therapy. The objectives of this study are to determine the resistance profile of microorganisms that cause bacteraemia of abdominal origin and to identify whether the previous use of antibiotics and the place of acquisition of bacteraemia are risk factors associated with the presence of resistant organisms. Material and methods A clinical, observational, epidemiological, retrospective cohort study was conducted with all the adult patients admitted to a university hospital from 2011 to 2013. Antimicrobial resistance profiles were described and a 95% confidence interval c…
Immune response to tick-borne hemoparasites: Host adaptive immune response mechanisms as potential targets for therapies and vaccines
2020
This article belongs to the Section Molecular Immunology.
A New Niche for Anoxygenic Phototrophs as Endoliths
2018
ABSTRACT Anoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here, we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-throughput sequencing of endolithic community DNA revealed the presence of abundant phylotypes potentially belonging to well-known APB clades. An ad hoc phylogenetic classification of these sequences enabled us to refine the assignments more stringently. Even then, all locations contained such putative APBs, often reaching a significant pro…
Effect of high pressure on the antimicrobial activity and secondary structure of the bacteriocin nisin
2018
International audience; Effect of high pressure (HP) treatment on the antimicrobial properties and the structure of nisin was evaluated. Nisin solutions at pH 2.8 or 6.1 were treated by HP at 500 MPa – 10 min – 20 °C and their antimicrobial potency was determined. It appeared that HP clearly impacted the antimicrobial activity of nisin, with respective activity loss of 22.5% and 49.9% at pH 2.8 and 6.1. Structural analysis of nisin by circular dichroism and Fourier transform-infrared spectroscopies revealed that the decrease of nisin antimicrobial activity was likely due to the unfolding of the protein induced by HP. A loss of nisin β-turns structure, particularly significant at neutral pH,…
The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures
2021
AbstractCitrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota have been characterized, while seed microbiota is still unknown. Bacterial and fungal endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi—belonging to Aspergillus, Quambalaria and Bjerkandera genera—and bacteria—belonging to Staphylococcus genus—were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions fr…