Search results for "microbial communities"
showing 10 items of 49 documents
Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at inte…
2014
The minimum information about a biofilm experiment (MIABiE) initiative has arisen from the need to find an adequate and scientifically sound way to control the quality of the documentation accompanying the public deposition of biofilm-related data, particularly those obtained using high-throughput devices and techniques. Thereby, the MIABiE consortium has initiated the identification and organization of a set of modules containing the minimum information that needs to be reported to guarantee the interpretability and independent verification of experimental results and their integration with knowledge coming from other fields. MIABiE does not intend to propose specific standards on how biof…
Editorial: Elevation Gradients: Microbial Indicators of Climate Change?
2019
Re-Clustering tool using an Open-Reference method that improves OTU definition
2019
International audience; 1.Environmental microbial communities are now widely studied using metabarcoding approaches, thanks to the democratization of high‐throughput DNA sequencing technologies. The massive number of reads produced with these technologies requires bioinformatic solutions to be treated. A key step in the analysis is to cluster reads into Operational Taxonomic Units (or OTUs) and thus reduce the amount of data for downstream analyses. Due to the important impact of the clustering method on the quantity and quality of OTUs, finding an equilibrium between the reliability and time‐consuming nature of the chosen strategy is a real challenge. The present article proposes a new pos…
Incidence and survival of human pathogens in French soils, impact of land use, pedoclimatic and biologic soil factors
2013
Soil contamination by bacterial pathogens can occur through manure, sewage sludge spreading or irrigation using waste water treatment plants effluents. Agricultural soils may act as reservoirs for these pathogens, play a significant role in their dissemination, leading to the potential contamination of food and water resources. Health risk associated with the occurrence of pathogens in environmental matrices has to be thoroughly evaluated. In this context, the objectives of this work were: i) to determine the prevalence of two pathogenic bacterial species (Listeria monocytogenes and Enterococcus faecalis) in a large collection of French soils originated from a systematic soil survey of the …
Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong li…
2006
International audience; The genetic structure of bacterial and fungal communities was characterized in the rhizosphere of Medicago truncatula Gaertn. cv. Jemalong line J5 at five developmental stages (three vegetative and two reproductive stages), and in three compartments (bulk soil, rhizosphere soil and root tissues). The genetic structure of microbial communities was determined by cultivation-independent methods using directly extracted DNA that was characterized by automated ribosomal intergenic spacer analysis (ARISA). Principal component analyses (PCA) indicate that, for all developmental stages, the genetic structure of microbial communities differed significantly by compartment, wit…
Potential for microbial diuron mineralisation in a small wine-growing watershed: from treated plots to lotic receiver hydrosystem
2009
BACKGROUND: Since biological degradation processes are known to be a major driver of the natural attenuation of pesticide residues in the environment, microbial communities adapted to pesticide biodegradation are likely to play a key environmental role in reducing pesticide exposure in contaminated ecosystems. The aim of this study was to assess the diuron-mineralising potential of microbial communities at a small-scale watershed level, including a diuron-treated vineyard (pollution source), its associated grass buffer strip (as a river protection area against pesticide runoff) and the lotic receiver hydrosystem (sediments and epilithon), by using radiorespirometry. RESULTS: Comparison of r…
Evidence de l'adaptation des communautés microbiennes sédimentaires de rivière à la minéralisation du diuron: influence du ruissellement et de l'éros…
2010
International audience; Purpose Surface runoff and erosion are major drivers of pesticide transport from soils to rivers draining vineyard watersheds. A recent study showed that applications of diuron on vineyards and diuron dispersal could lead to microbial adaptation to diuron biodegradation from treated soils to the receiving hydrosystem. Given the limited knowledge on microbial adaptation to pesticide degradation in aquatic environments, we conducted a microcosm study designed to assess the impact of runoff and erosion processes on the adaptation of riverine-sediment microbial communities to diuron mineralization. Materials and methods The experimental laboratory set-up consisted in aqu…
Effects of the introduction of a biocontrol strain of Trichoderma atroviride on non target soil micro-organisms
2009
International audience; The main objective of this study was to assess the impact of the application of an antagonistic strain of Trichoderma atroviride on the native microbial soil communities. The structures of the fungal and bacterial communities were assessed by T-RFLP (terminal restriction fragment length polymorphism) method, based on T-RFLP analysis of 18S and 16S rRNA genes, respectively. Results showed that the introduction of the strain I-1237 into two soils slightly modified the microbial diversity, only for a short period of time. Nine months post-inoculation resilience took place, resulting in similar structures of the fungal and bacterial communities in the inoculated and cont…
Contamination of soil by copper affects the dynamics, diversity, and activity of soil bacterial communities involved in wheat decomposition and carbo…
2009
ABSTRACT A soil microcosm experiment was conducted to evaluate the influence of copper contamination on the dynamics and diversity of bacterial communities actively involved in wheat residue decomposition. In the presence of copper, a higher level of CO 2 release was observed, which did not arise from greater wheat decomposition but from a higher level of stimulation of soil organic matter mineralization (known as the priming effect). Such functional modifications may be related to significant modifications in the diversity of active bacterial populations characterized using the DNA stable-isotope probing approach.
Microbial Biofilms Along a Geochemical Gradient at the Shallow-Water Hydrothermal System of Vulcano Island, Mediterranean Sea
2022
Shallow water hydrothermal vents represent highly dynamic environments where strong geochemical gradients can shape microbial communities. Recently, these systems are being widely used for investigating the effects of ocean acidification on biota as vent emissions can release high CO2 concentrations causing local pH reduction. However, other gas species, as well as trace elements and metals, are often released in association with CO2 and can potentially act as confounding factors. In this study, we evaluated the composition, diversity and inferred functional profiles of microbial biofilms in Levante Bay (Vulcano Island, Italy, Mediterranean Sea), a well-studied shallow-water hydrothermal ve…