Search results for "intergenic spacer"
showing 10 items of 32 documents
Impact of inoculation with the phytostimulatory PGPR Azospirillum lipoferum CRT1 on the genetic structure of the rhizobacterial community of field-gr…
2009
International audience; The phytostimulatory PGPR Azospirillum lipoferum CRT1 was inoculated to maize seeds and the impact on the genetic structure of the rhizobacterial community in the field was determined during maize growth by Automated Ribosomal Intergenic Spacer Analysis (ARISA) of rhizosphere DNA extracts. ARISA fingerprints could differ from one plant to the next as well as from one sampling to the next. Inoculation with strain CRT1 enhanced plant-to-plant variability of the ARISA fingerprints and caused a statistically significant shift in the composition of the indigenous rhizobacterial community at the first two samplings. This is the first study on the ecological impact of Azosp…
Evidence for shifts in the structure and abundance of the microbial community in a long-term PCB-contaminated soil under bioremediation.
2011
International audience; Although the impact of bioremediation of PCB-contaminated sites on the indigenous microbial community is a key question for soil restoration, it remains poorly understood. Therefore, a small-scale bioremediation assay made of (a) a biostimulation treatment with carvone, soya lecithin and xylose and (b) two bioaugmentation treatments, one with a TSZ7 mixed culture and another with a Rhodococcus sp. Z6 pure strain was set up. Changes in the structure of the global soil microbial community and in the abundances of different taxonomic phyla were monitored using ribosomal intergenic spacer analysis (RISA) and real-time PCR. After an 18-month treatment, the structure of th…
The Root Mycobiota of Betula aetnensis Raf., an Endemic Tree Species Colonizing the Lavas of Mt. Etna (Italy)
2021
Betula aetnensis is an endemic tree of high conservation value, which thrives on the nutrient-poor volcanic soils of Mount Etna. Since plant–microbe interactions could play a crucial role in plant growth, resource uptake, and resistance to abiotic stresses, we aimed to characterize the root and rhizosphere microbial communities. Individuals from natural habitat (NAT) and forest nursery (NURS) were surveyed through microscopy observations and molecular tools: bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA), fungal denaturing gradient gel electrophoresis (DGGE). B. aetnensis was found to be simultaneously colonized by arbuscular (AM), ectomycorrhizal (ECM), ericoid…
Phylogenetic relationships among tetraploid species of Bellevalia (Asparagaceae) endemic to south-central Mediterranean
2017
AbstractIn the south-central Mediterranean four tetraploid species of Bellevalia occur: B. dolichophylla, B. galitensis, B. mauritanica, and B. pelagica. Another group of plants, morphologically similar to B. dolichophylla, has been recently recovered in Zembra Island (Tunisia). A phylogenetic reconstruction involving all these tetraploid taxa was performed using both plastidial and nuclear markers (trnL-trnF and ITS, respectively). For all these taxa, an allopolyploid origin involving B. romana and B. dubia is supported. Regarding plants from Zembra, they may fall within the variability of B. dolichophylla.
Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodologic…
2001
ABSTRACT Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extracti…
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…
Comparison of different primer sets for use in Automated Ribosomal Intergenic Spacer Analysis of complex bacterial communities.
2004
ABSTRACT ITSF and ITSReub, constituting a new primer set designed for the amplification of the 16S-23S rRNA intergenic transcribed spacers, have been compared with primer sets consisting of 1406F and 23Sr (M. M. Fisher and E. W. Triplett, Appl. Environ. Microbiol. 65:4630-4636, 1999) and S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 (L. Ranjard et al., Appl. Environ. Microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (ARISA) of complex bacterial communities. An agricultural soil and a polluted soil, maize silage, goat milk, a small marble sample from the façade of the Certosa of Pavia (Pavia, Italy), and brine from a deep hypersaline anoxi…
Cumulative Effects of Short-Term Polymetal Contamination on Soil Bacterial Community Structure
2006
ABSTRACT In this study we evaluated the short-term effects of copper, cadmium, and mercury, added singly or in combination at different doses, on soil bacterial community structure using the bacterial automated ribosomal intergenic spacer analysis (B-ARISA) fingerprinting technique. Principal-component analysis of B-ARISA profiles allowed us to deduce the following order of impact: (Cu + Cd + Hg) >> Hg ≥ Cd > Cu. These results demonstrated that there was a cumulative effect of metal toxicity. Furthermore, the trend of modifications was consistent with the “hump-backed” relationships between biological diversity and disturbance described by Giller et al. (K. E. Giller, E. Witler, an…
Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in…
2006
The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modi…
Soil DNA evidence for altered microbial diversity after long-term application of municipal wastewater
2010
International audience; Water resources constitute a social, agricultural and economic problem in most countries of the southern Mediterranean Basin. Alternative strategies have been developed such as the reuse of municipal wastewater for irrigation in agriculture. Despite numerous advantages for soil fertility and crop productivity, recycling wastewater in soils also has several ecotoxicological and sanitary problems. Few investigations have assessed the risk by evaluating the impact of wastewater irrigation on soil microbes. Here, we report for the first time the short- and long-term effects of treated municipal wastewater irrigation on the density and genetic structure of bacterial and f…