Separation of acid-soluble constituents of soil humic acids by dissolution in alkaline urea solution and precipitation with acid

Aoyama, Masakazu

doi:10.1186/s40538-015-0041-5

Cited by 4 publications

(1 citation statement)

References 28 publications

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“…In this study, soil extract prepared by mixing nematode-free field soil with Tris EDTA (TE) buffer was used for evaluating the performance of soil inhibitors in ddPCR. TE buffer (pH 8.0) was used for this purpose since humic acids are soluble in neutral and alkaline pH, whereas fulvic acid is soluble in all pH [ 50 , 52 ]. Moreover, TE is one of the common buffers used for DNA elution and long-term storage of DNA.…”

Section: Discussionmentioning

confidence: 99%

Assessment of Common Factors Associated with Droplet Digital PCR (ddPCR) Quantification of Paratrichodorus allius in Soil

Lawaju,

Yan

2024

IJMS

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This research investigated the factors associated with the quantitative detection of Paratrichodorus allius in soil using droplet digital PCR (ddPCR). Small-sized nematodes exhibited significantly lower DNA quantities compared to their medium and large counterparts. Soil pre-treatments (room temperature drying and 37 °C oven-drying) demonstrated no substantial impact on ddPCR detection, and soil storage (0–3 months at 4 °C) exhibited negligible alterations in DNA quantities. A commercial DNA purification kit improved the resulting quality of ddPCR, albeit at the cost of a notable reduction in DNA quantity. Upon assessing the impact of inhibitors from soil extracts, a higher inhibitor concentration (5%) influenced ddPCR amplification efficiency. Incorporating bovine serum albumin (BSA) (0.2 μg/μL or 0.4 μg/μL) into the ddPCR setup mitigated the issue. In brief, while ddPCR exhibits minimal sensitivity to soil pre-treatments and storage, higher concentrations of PCR inhibitors and the DNA purification process can influence the results. Despite ddPCR’s capability to detect nematodes of all sizes, quantification may not precisely reflect soil population. Incorporating BSA into the ddPCR setup enhances both detection and quantification capacities. This study represents the first comprehensive investigation of its kind for plant-parasitic nematodes, providing crucial insights for application of ddPCR in nematode diagnosis directly from the soil DNA.

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Section: Discussionmentioning

confidence: 99%