DGGE and RISA Protocols for Microbial Community Analysis in Soil

Solaiman, Zakaria; Marschner, Petra

doi:10.1007/978-3-540-70865-0_11

Cited by 5 publications

(6 citation statements)

References 13 publications

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“…To amplify specific 18S rRNA of fungi from soils for DGGE, nested PCR was performed (Solaiman and Marschner (2007). The PCR reaction mixture was set up in 50 μL, containing 1 μmol of MgCl 2 , 200 μmol of each dNTP, 0.5 μmol of each primer, 5 μL of template DNA, 5 μL of 10 × PCR buffer and 2.5 U of Ex Taq TM polymerase (TaKaRa Inc., Dalian, China).…”

Section: Rhizobox Design and The Planting Experimentmentioning

confidence: 99%

“…A protocol modified by Solaiman and Marschner (2007) was used in soil total DNA extraction. Briefly, the DNA was liberated from the microbial cells by homogenization with freezing-thawing in the presence of phosphate buffer and sodium dodecyl sulfate (SDS).…”

Section: Rhizobox Design and The Planting Experimentmentioning

confidence: 99%

“…10: 438-443 doi: 10.17221/94/2015-PSE 72°C for 40 s, for 38 cycles, followed by 72°C for 10 min, and finally hold at 4°C constant. A modified touch-down PCR procedure was used for fungal cycling amplification (Solaiman and Marschner 2007). All PCR products were electrophoresed on 1.5% (w/v) agarose to verify their size and quality.…”

Section: Rhizobox Design and The Planting Experimentmentioning

confidence: 99%

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Tree species composition influenced microbial diversity and nitrogen availability in rhizosphere soil

Liu¹,

Liu²,

Fang³

et al. 2015

PLANT SOIL ENVIRON

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A greenhouse experiment was conducted to evaluate effects of monoculture and mixed planting of three tree species on microbial diversity and nitrogen (N) availability in rhizosphere and bulk soils. Six treatments with poplar, willow, and alder mono-or mixed seedlings were grown in the rhizoboxes and both rhizosphere and bulk soils were sampled and analysed after eight-month growth. Microbial diversity in rhizosphere soil was significantly higher than in bulk soils based on denatured gradient gel electrophoresis (DGGE) fingerprinting of 16S-or 18S-rRNA gene fragments of soil microbial community. Tree species composition significantly influenced microbial diversity index and nitrogen contents in the rhizosphere soil, with the highest values of genotypic richness, Shannon diversity index and inorganic nitrogen contents were observed in rhizosphere soils of poplar-alder mixture. Shannon diversity indices of bacteria and fungi in the rhizosphere soils were positively and significantly correlated with nitrogen contents. Alder addition significantly improved genotypic richness, microbial diversity index and nitrogen availability in the rhizosphere soils, suggesting that adding N-fixing alder into poplar plantations is a good option in the practice. 438Vol. 61, 2015, No. 10: 438-443 Plant Soil Environ.doi: 10.17221/94/2015-PSE Poplar is one of the most promising short rotation plantation forest species and at present, the area of poplar plantation in China has reached about 8.5 million ha. However, monoculture plantations lead to declines in soil fertility and plant biomass productivity over successive rotations (Mao et al. 2010). Therefore, mixed plantations have been recommended to combat soil degradation and maintain productivity of poplar plantations. In this study, a greenhouse experiment was conducted to evaluate the effect of monoculture and mixed plantations of three tree species on rhizosphere microbial diversity and nitrogen (N) availability. We hypothesized that rhizosphere effects on soil microbial diversity and nitrogen availability would vary with tree species and their compositions due to differences in intrinsic biological characteristics and complementarities of species traits (especially ecological characteristics). The specific objectives were to: (1) assess effects of tree species compositions on diversity of bacteria and fungi and nitrogen availability in rhizospheric and non-rhizospheric soils, and (2) discuss the relationships between soil microbial diversity and nitrogen availability. MATERIAL AND METHODS Rhizobox design and the planting experiment.The rhizoboxes were made of two top-open black Plexiglas compartments separated by a polyamide membrane with 30 µm pore-diameters and 75 µm thick (Fang et al. 2013). The plant-root compartment was 250 mm wide and had an internal volume of 22.5 L. The sampling compartment, where rhizosperic and bulk soils were sampled, was 50 mm wide and had an internal volume of 4.5 L. The soil used in the rhizoboxes had pH 7.2 and content of organic carbon ...

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Section: Rhizobox Design and The Planting Experimentmentioning

confidence: 99%

Section: Rhizobox Design and The Planting Experimentmentioning

confidence: 99%

Section: Rhizobox Design and The Planting Experimentmentioning

confidence: 99%

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Tree species composition influenced microbial diversity and nitrogen availability in rhizosphere soil

Liu¹,

Liu²,

Fang³

et al. 2015

PLANT SOIL ENVIRON

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“…Amplicons from gradient fractions were generated with the primers 341f-GC and 534r as described previously (49). Denaturing gradient gel electrophoresis (DGGE) was performed using the DGGEEK-2001 system (C.B.S.…”

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confidence: 99%

“…Scientific, Solana Beach, CA). PCR products (30 l) were loaded on 8% (vol/vol) polyacrylamide gels with a 30 to 70% denaturant gradient (49), and electrophoresis was carried out at 60°C for 16 h at 70 V. Gels were imaged after staining with GelRed (Biotium, Inc., Hayward, CA) for 1 h. Selected bands were excised and reamplified with the primers 341f and 534r.…”

mentioning

confidence: 99%

Cultivation-Independent Detection of Autotrophic Hydrogen-Oxidizing Bacteria by DNA Stable-Isotope Probing

Pumphrey

Ranchou-Peyruse

Spain

2011

Appl Environ Microbiol

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Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of 13 CO 2 was H 2 dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from 13 C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H 2 concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.

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Microbiota potentialized larvicidal action of imidazolium salts against Aedes aegypti (Diptera: Culicidae)

Júnior

Lemos

Almeida

et al. 2019

Sci Rep

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Mosquitoes are important vectors of pathogens due to their blood feeding behavior. Aedes aegypti (Diptera: Culicidae) transmits arboviruses, such as dengue, Zika, and Chikungunya. This species carries several bacteria that may be beneficial for its biological and physiological development. Therefore, studying the response of its microbiota to chemical products could result in vector control. Recently, imidazolium salts (IS) were identified as effective Ae. aegypti larvicides. Considering the importance of the mosquito microbiota, this study addressed the influence of IS on the bacteria of Ae. aegypti larvae. After exposition of larvae to different IS concentrations, the cultured microbiota was identified through culturomics and mass spectrometry, and the non-cultivated microbiota was characterized by molecular markers. In addition, the influence of the IS on axenic larvae was studied for comparison. There was an alteration in both cultivable species and in their diversity, including modifications in bacterial communities. The axenic larvae were less susceptible to the IS, which was increased after exposing these larvae to bacteria of laboratory breeding water. This highlights the importance of understanding the role of the larval microbiota of Ae. aegypti in the development of imidazolium salt-based larvicides. Such effect of IS towards microbiota of Ae. aegypti larvae, through their antimicrobial action, increases their larvicidal potential.

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DGGE and RISA Protocols for Microbial Community Analysis in Soil

Cited by 5 publications

References 13 publications

Tree species composition influenced microbial diversity and nitrogen availability in rhizosphere soil

Tree species composition influenced microbial diversity and nitrogen availability in rhizosphere soil

Cultivation-Independent Detection of Autotrophic Hydrogen-Oxidizing Bacteria by DNA Stable-Isotope Probing

Microbiota potentialized larvicidal action of imidazolium salts against Aedes aegypti (Diptera: Culicidae)

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