The Influence of Soil Organic Matter on DNA Adsorptions on Andosols

Saeki, Kazutoshi; Sakai, Masao

doi:10.1264/jsme2.me09117

Cited by 35 publications

(27 citation statements)

References 22 publications

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“…Clay minerals and hydroxides have the capacity to facilitate selforganization and condensation polymerization. Clays tend to adsorb organic molecules strongly (e.g., Saeki and Sakai, 2009), and this contributes to their ability to catalyze a diversity of organic reactions, such as RNA formation and elongation on montmorillonite clay (Ferris et al, 1996).…”

Section: Adsorption Of Organics To Minerals: the Origin Of Life And Pmentioning

confidence: 99%

The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond

Röling¹,

Aerts²,

Patty³

et al. 2015

Astrobiology

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The detection of biomarkers plays a central role in our effort to establish whether there is, or was, life beyond Earth. In this review, we address the importance of considering mineralogy in relation to the selection of locations and biomarker detection methodologies with characteristics most promising for exploration. We review relevant mineral-biomarker and mineral-microbe interactions. The local mineralogy on a particular planet reflects its past and current environmental conditions and allows a habitability assessment by comparison with life under extreme conditions on Earth. The type of mineral significantly influences the potential abundances and types of biomarkers and microorganisms containing these biomarkers. The strong adsorptive power of some minerals aids in the preservation of biomarkers and may have been important in the origin of life. On the other hand, this strong adsorption as well as oxidizing properties of minerals can interfere with efficient extraction and detection of biomarkers. Differences in mechanisms of adsorption and in properties of minerals and biomarkers suggest that it will be difficult to design a single extraction procedure for a wide range of biomarkers. While on Mars samples can be used for direct detection of biomarkers such as nucleic acids, amino acids, and lipids, on other planetary bodies remote spectrometric detection of biosignatures has to be relied upon. The interpretation of spectral signatures of photosynthesis can also be affected by local mineralogy. We identify current gaps in our knowledge and indicate how they may be filled to improve the chances of detecting biomarkers on Mars and beyond.

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Section: Adsorption Of Organics To Minerals: the Origin Of Life And Pmentioning

confidence: 99%

The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond

Röling¹,

Aerts²,

Patty³

et al. 2015

Astrobiology

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“…These soils were classified as Typic Melanudands. The properties of andosols were indicated in previous studies (28,29).…”

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confidence: 78%

“…The adsorption of DNA by phyllosilicate minerals can differ from that by variable-charge soils such as andosol. There have been several studies on the retention of DNA in natural soils (18,19,26,28,29).Tris(hydroxymethyl)aminomethane (Tris) solutions are used widely as buffers due to their stabilizing effects on biomolecules (16). There have been several studies about the adsorption of DNA on soil particles using Tris-HCl buffers as background solutions (e.g.…”

mentioning

confidence: 99%

“…These soils were classified as Typic Melanudands. The properties of andosols were indicated in previous studies (28,29).We used salmon sperm dsDNA at 10 mg mL −1 (average molecular size, 1000 bp) purchased from Invitrogen (California, USA); DNA solutions were prepared with distilled water prior to adsorption experiments. The Tris-HCl buffer (pH 7.0) was prepared by adjusting a 1 M Tris solution to pH 7.0 with concentrated HCl.…”

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Effect of Tris-HCl Buffer on DNA Adsorption by a Variety of Soil Constituents

2011

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We investigated the effect of tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl) buffer (pH 7.0) as a bulk solution on the adsorption of DNA by gibbsite, goethite, montmorillonite, kaolinite, synthetic and natural allophanes, two humic acids and two andosols. The natural allophane, gibbsite, kaolinite and an andosol adsorbed significantly more DNA in a 0.1 M Tris-HCl buffer than in a 0.1 M NaCl solution (t-test, P<0.005). In contrast, montmorillonite adsorbed significantly less DNA in the Tris-HCl than NaCl solution (P<0.05). Care should be taken when using TrisHCl in studies on the adsorption of extracellular DNA molecules by soil particles.Key words: DNA adsorption, Tris-HCl buffer, allophane, soil, montmorilloniteNucleic acid adsorption at soil-solution interfaces is important in understanding many subjects such as the biosafety of genetically modified organisms (17), protection of DNA against nucleases in soil (13, 22), genetic transformation of competent bacteria in situ (5,6,11,22) and extraction of DNA from soil for the study of microbial communities (e.g. 34).The adsorption of DNA molecules by phyllosilicate minerals is affected by several factors including DNA size (6), mineral types (2), the pH of buffer solutions (7,8,11), the ionic strength of solutions (12), the presence of other cellular components (21, 22) and electrolytes (7). The adsorption of DNA by phyllosilicate minerals can differ from that by variable-charge soils such as andosol. There have been several studies on the retention of DNA in natural soils (18,19,26,28,29).Tris(hydroxymethyl)aminomethane (Tris) solutions are used widely as buffers due to their stabilizing effects on biomolecules (16). There have been several studies about the adsorption of DNA on soil particles using Tris-HCl buffers as background solutions (e.g. 2, 3, 4). Recently, Wei et al. (36) reported that a Tris-HCl buffer (pH 7.4) increased protein adsorption on germanium (Ge) surface. To grasp how much Tris-HCl affects on the adsorption of DNA by soils, we investigated the effect of a Tris-HCl buffer (pH 7.0) as a bulk solution on DNA adsorption by a variety of materials (gibbsite, goethite, montmorillonite, kaolinite, synthetic and natural allophanes, two humic acids and two andosols).The mineral samples used in this study were: Gibbsite, provided by Showa Denko (Tokyo, Japan); goethite, synthesized by the method of Atkinson et al.(1); montmorillonite K10, provided by Sigma-Aldrich (St Louis, USA); kaolinite, collected from Iriki, Kagoshima, Japan; a synthetic allophane produced by the method of Ohashi et al. (20) and a natural allophane supplied by Shinagawa Chemicals (Tokyo, Japan). The properties of these solids have been reported recently (14,24,25). Humic acid A and B were purified from reagents provided by Wako Pure Chemical Industries (Osaka, Japan) and Sigma-Aldrich. The purification process was based on the IHSS method (33). The properties of humic acids were described previously (10,15,27). Two surface humic andosols were also used; Chiran soil (CR ...

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Persistence and degradation of Phytophthora cinnamomi DNA and RNA in different soil types

et al. 2020

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DNA and RNA detected in soil using molecular techniques may originate from a living or dead organism. It is therefore of interest to know how long the DNA and RNA from a decaying organism can persist in soil, and how environmental conditions such as soil temperature, moisture, and microbial populations impact on the survival time. This study determined the difference between the persistence of Phytophthora cinnamomi mRNA and DNA in different soil types. DNA and RNA were extracted from P. cinnamomi and 10 ng/250 mg of soil was applied to five different soil types that were either air‐dried or maintained at 70% field capacity. The persistence of DNA at 20°C was tested after intervals of 0, 3, 7, 14, 90, 241, and 378 days, and for RNA at 0, 1, 3, and 7 days using qPCR and RT‐qPCR techniques, respectively. Persistence was longer in dry than moist soil, P. cinnamomi DNA could be readily detected in dry soil conditions for up to 90 days and was found at extremely low levels at 241 and 378 days. RNA was detected only on day 1, except for dry river sand, and moist sandy loam in which it persisted for 3 days; it was not detected after seven days. These results confirm that RNA degrades very quickly, making it a valuable tool for determining the presence of viable Phytophthora in soil. In contrast, DNA can be remarkably stable in some environments, and positive results could be obtained even after the death of the organism for a year or more prior to the test. For diagnostics, the use of an RNA‐based test avoids the possibility of such false positive results. In the context of the research project, this study is relevant to determining how long viable Phytophthora remains in soil after the eradication protocols have been instigated. In a broader context, the persistence of DNA is relevant to any study using environmental DNA for diagnostics or for metabarcoding when undertaking community ecology or microbiome studies. These results are relevant for studies using detection of P. cinnamomi nucleic acids in soils for purposes of diagnostics, ecological research, or projects on eradication.

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The Influence of Soil Organic Matter on DNA Adsorptions on Andosols

Cited by 35 publications

References 22 publications

The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond

The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond

Effect of Tris-HCl Buffer on DNA Adsorption by a Variety of Soil Constituents

Persistence and degradation of Phytophthora cinnamomi DNA and RNA in different soil types

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