The genotypic diversity of Pseudomonas brassicacearum populations isolated from roots of Arabidopsis thaliana: influence of plant genotype

Fromin, Nathalie; Achouak, Wafa; Thiéry, J.M.; Heulin, Thierry

doi:10.1111/j.1574-6941.2001.tb00849.x

Cited by 36 publications

(31 citation statements)

References 39 publications

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“…The presence of certain bands migrating at the same level in DGGE profiles derived from heavy and light DNA fractions were analysed, and obtained sequences were identical, suggesting that multiple genotypes of the same species can occur in a single soil, as reported in relation to crop management (Achouak et al, 2000) and in Arabidopsis thaliana and wheat rhizospheres (Fromin et al, 2001). Our results provide evidence that certain genotypes are assimilating root exudates, whereas others benefit directly from refractory SOM or from compounds derived from SOM partially degraded by specialized bacteria.…”

Section: Priming Effectmentioning

confidence: 82%

Plant host habitat and root exudates shape soil bacterial community structure

et al. 2008

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The rhizosphere is active and dynamic in which newly generated carbon, derived from root exudates, and ancient carbon, in soil organic matter (SOM), are available for microbial growth. Stable isotope probing (SIP) was used to determine bacterial communities assimilating each carbon source in the rhizosphere of four plant species. Wheat, maize, rape and barrel clover (Medicago truncatula) were grown separately in the same soil under 13 CO 2 (99% of atom 13 C) and DNA extracted from rhizosphere soil was fractionated by isopycnic centrifugation. Bacteria-assimilating root exudates were characterized by denaturing gradient gel electrophoresis (DGGE) analysis of 13 C-DNA and root DNA, whereas those assimilating SOM were identified from 12 C-DNA. Plant species root exudates significantly shaped rhizosphere bacterial community structure. Bacteria related to Sphingobacteriales and Myxococcus assimilated root exudates in colonizing roots of all four plants, whwereas bacteria related to Sphingomonadales utilized both carbon sources, and were identified in light, heavy and root compartment DNA. Sphingomonadales were specific to monocotyledons, whereas bacteria related to Enterobacter and Rhizobiales colonized all compartments of all four plants, used both fresh and ancient carbon and were considered as generalists. There was also evidence for an indirect important impact of root exudates, through stimulation of SOM assimilation by a diverse bacterial community.

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Section: Priming Effectmentioning

confidence: 82%

Plant host habitat and root exudates shape soil bacterial community structure

et al. 2008

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“…For the BOX fingerprints, band positions on each gel were normalized with the 1-kb size ladder as an external reference standard. Only DNA fragments ranging from 2,036 bp to 506 bp were used in the analysis (17). The bands were assigned to band classes, which resulted in transformation of a fingerprint into a binary table (0, absent in band class; 1, present in band class).…”

Section: Methodsmentioning

confidence: 99%

Use of 16S-23S rRNA Intergenic Spacer Region PCR and Repetitive Extragenic Palindromic PCR Analyses of Escherichia coli Isolates To Identify Nonpoint Fecal Sources

Seurinck

Verstraete

Siciliano

2003

Appl Environ Microbiol

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Despite efforts to minimize fecal input into waterways, this kind of pollution continues to be a problem due to an inability to reliably identify nonpoint sources. Our objective was to find candidate source-specific Escherichia coli fingerprints as potential genotypic markers for raw sewage, horses, dogs, gulls, and cows. We evaluated 16S-23S rRNA intergenic spacer region (ISR)-PCR and repetitive extragenic palindromic (rep)-PCR analyses of E. coli isolates as tools to identify nonpoint fecal sources. The BOXA1R primer was used for rep-PCR analysis. A total of 267 E. coli isolates from different fecal sources were typed with both techniques. E. coli was found to be highly diverse. Only two candidate source-specific E. coli fingerprints, one for cow and one for raw sewage, were identified out of 87 ISR fingerprints. Similarly, there was only one candidate source-specific E. coli fingerprint for horse out of 59 BOX fingerprints. Jackknife analysis resulted in an average rate of correct classification (ARCC) of 83% for BOX-PCR analysis and 67% for ISR-PCR analysis for the five source categories of this study. When nonhuman sources were pooled so that each isolate was classified as animal or human derived (raw sewage), ARCCs of 82% for BOX-PCR analysis and 72% for ISR-PCR analysis were obtained. Critical factors affecting the utility of these methods, namely sample size and fingerprint stability, were also assessed. Chao1 estimation showed that generally 32 isolates per fecal source individual were sufficient to characterize the richness of the E. coli population of that source. The results of a fingerprint stability experiment indicated that BOX and ISR fingerprints were stable in natural waters at 4, 12, and 28°C for 150 days. In conclusion, 16S-23S rRNA ISR-PCR and rep-PCR analyses of E. coli isolates have the potential to identify nonpoint fecal sources. A fairly small number of isolates was needed to find candidate source-specific E. coli fingerprints that were stable under the simulated environmental conditions.

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“…Briefly, 1 g of fresh weight root or soil was crushed in 10 mL SPB. The root and soil suspensions were 10-fold serially diluted in SPB and spread on mS1 medium, which is selective for Pseudomonas [19,52]. Colonyforming units (cfu) were determined after 72 h of incubation at 24°C.…”

Section: Pseudomonas Isolationmentioning

confidence: 99%

Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

et al. 2005

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A total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO 2 content (pCO 2 ) at the Swiss FACE (Free Air CO 2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil-associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO 2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO 2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO 2 . Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO 2 treatment.

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The genotypic diversity of Pseudomonas brassicacearum populations isolated from roots of Arabidopsis thaliana: influence of plant genotype

Cited by 36 publications

References 39 publications

Plant host habitat and root exudates shape soil bacterial community structure

Plant host habitat and root exudates shape soil bacterial community structure

Use of 16S-23S rRNA Intergenic Spacer Region PCR and Repetitive Extragenic Palindromic PCR Analyses of Escherichia coli Isolates To Identify Nonpoint Fecal Sources

Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

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