Soil microbial community analysis in the environmental risk assessment of transgenic plants

Ikeda, Seishi; Ytow, Nozomi; Ezura, Hiroshi; Minamisawa, Kiwamu; Fujimura, Tatsuhito

doi:10.5511/plantbiotechnology.23.137

Cited by 18 publications

(17 citation statements)

References 120 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Furthermore, in many cases the differences between rhizosphere microbial communities integrated with transgenic plants and parental non-transgenic plants showed to be temporary and dependent on the presence of live plants (Dunfield & Germida 2003). Despite some inherent limitations, the use of the culture-dependent methods based on plate counts on selective media for specific groups of soil microorganisms, such as fungi and bacteria, has provided useful information for evaluating microbial diversity in various environmental samples, including the risk assessment of transgenic plants (Ikeda et al 2006). …”

Section: Carbon Substrate Utilization Pattern Analysismentioning

confidence: 99%

See 1 more Smart Citation

Effect of transgenic alfalfa plants with introduced gene for Alfalfa Mosaic Virus coat protein on rhizosphere microbial community composition and physiological profile

2011

View full text Add to dashboard Cite

The aim of this study was to evaluate the effect of transgenic alfalfa (Medicago sativa L.) plants, in comparison to their non-transgenic counterpart, on the density and physiological profiles of aerobic bacteria in the rhizosphere. Plants of transgenic alfalfa expressing the AMVcp-s gene coding for Alfalfa Mosaic Virus coat protein were cultivated in a climatic chamber. Two methods were used to determine the microbial diversity in rhizospheres of transgenic plants. First, the cultivation-dependent plating method, based on the determination of the density of colony-forming bacteria, and second, a biochemical method using the Biolog TM system, based on the utilization of different carbon sources by soil microorganisms. Statistically significant differences in densities of rhizospheric bacteria between transgenic and non-transgenic alfalfa clones were observed in ammonifying bacteria (GTL4/404-1), cellulolytic bacteria (GTL4/404-1, GTL4/402-2, A5-3-3), rhizobial bacteria (GTL4/402-2), denitrifying bacteria (A5-3-3) and Azotobacter spp. (GTL4/402-2). The highest values of substrate utilization by microbial communities and average respiration of C-sources were determined in non-transgenic alfalfa plants of the isogenic line SE/22-GT2. Carbohydrates, carboxylic acids and amino-acids were the most utilized carbon substrates by both Gram-negative and Gram-positive bacteria. Both, the community metabolic diversity and the utilization of C-sources increased in all alfalfa lines with culture time and regardless of transgenic or non-transgenic nature of lines.

show abstract

Section: Carbon Substrate Utilization Pattern Analysismentioning

confidence: 99%

“…The evaluation of the impact of transgenic plants on soil microbial community requires sampling of rhizospheric soils (Ikeda et al 2006). The rhizosphere can be defined as the zone of primary root influence and it harbours very high numbers and activities of organisms (Giri et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Effect of transgenic alfalfa plants with introduced gene for Alfalfa Mosaic Virus coat protein on rhizosphere microbial community composition and physiological profile

2011

View full text Add to dashboard Cite

show abstract

“…However, the direct extraction of DNA is generally more difficult from soils than other environmental samples such as water. In addition, and despite much that has been reported on this issue, the generation of reliable nucleic acid preparations from soil matrices remains a challenging issue due to the extreme complexity of the physical, chemical and biological properties of soils 22) . One of the main problems associated with soil DNA extraction techniques appears to be the adsorption of DNA to the soil matrices 16) .…”

mentioning

confidence: 99%

Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol

et al. 2008

Self Cite

View full text Add to dashboard Cite

A series of additives were evaluated for their effects on improving the yield and quality of DNA extracted from recalcitrant soils. Levels of possible DNA contaminants in these supplements were also assessed. Three of the additives (skim milk, casein, and RNA) were shown to be effective in improving the stable extraction of DNA from recalcitrant samples of Andosol. However, whereas skim milk appeared to be the most effective additive for this purpose, our data indicated that this commercially sourced product contained considerable amounts of contaminant DNA (30 to 40 µg/g skim milk). A ribosomal intergenic spacer analysis (RISA) revealed the consistent contamination of different batches of this product with DNA of several species of both eukaryotes (cattle and protists) and prokaryotes. In particular, thermophilic bacteria such as Geobacillus and Anoxybacillus were identified in the sequenced PCR amplicons from skim milk. The results of the RISA clearly also indicated that the impact of contaminated DNA on the analysis of a microbial community could be significant when skim milk is used for extracting DNA from a recalcitrant soil. In contrast, only a trace amount of contaminating DNA was evident in casein and none was detected in the RNA examined in the present study.

show abstract

“…We therefore mainly focus on the relevant considerations when extracting DNA from the phytosphere in this review. The details of some of the DNA extraction procedures that can be used for recalcitrant environmental samples, such as rhizosphere soils, are referred to our recent review 47) .…”

Section: Dna Extractionmentioning

confidence: 99%

Microbial Community Analysis of the Phytosphere Using Culture-Independent Methodologies

et al. 2007

Self Cite

View full text Add to dashboard Cite

The phytosphere is an attractive habitat for microorganisms due to an abundance of nutrients and relative environmental stability. The microorganisms that occupy this habitat assist in the uptake of nutrients from soils and can exert considerable influence upon the overall health of the plant. Recent technical advances in environmental microbiology have enabled the tracing and assessment of these microorganisms using rapid and simple molecular techniques without any culture-dependent bias. We herein review the current status of these modern molecular techniques in the study of plant-associated microbes, and summarize the issues relevant to the phytosphere from the aspect of both basic and applied science.

show abstract

Soil microbial community analysis in the environmental risk assessment of transgenic plants

Cited by 18 publications

References 120 publications

Effect of transgenic alfalfa plants with introduced gene for Alfalfa Mosaic Virus coat protein on rhizosphere microbial community composition and physiological profile

Effect of transgenic alfalfa plants with introduced gene for Alfalfa Mosaic Virus coat protein on rhizosphere microbial community composition and physiological profile

Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol

Microbial Community Analysis of the Phytosphere Using Culture-Independent Methodologies

Contact Info

Product

Resources

About