DNA extraction efficiency from soil as affected by pyrolysis temperature and extractable organic carbon of high-ash biochar

2017 ◽  
Vol 115 ◽  
pp. 129-136 ◽  
Author(s):  
Zhongmin Dai ◽  
Tara M. Webster ◽  
Akio Enders ◽  
Kelly L. Hanley ◽  
Jianming Xu ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Dna Extraction ◽  
Extraction Efficiency ◽  
Pyrolysis Temperature

scholarly journals Fire-derived organic carbon in soil turns over on a centennial scale

2012 ◽  
Vol 9 (8) ◽  
pp. 2847-2857 ◽  
Author(s):  
N. Singh ◽  
S. Abiven ◽  
M. S. Torn ◽  
M. W. I. Schmidt
Keyword(s):  
Organic Carbon ◽  
Field Study ◽  
Carbon Emissions ◽  
Time Scale ◽  
Pyrolysis Temperature ◽  
Meta Analysis ◽  
Turnover Time ◽  
Pyrogenic Carbon ◽  
Centennial Time Scale ◽  
Slow Cycling

Abstract. Pyrogenic carbon (PyC), the residue of an incomplete combustion of biomass, is considered as a carbon (C) sink due to its assumed stability in soil. PyC turnover time estimated using two modelling approaches, based on data from 16 published studies (n = 54) on PyC degradation, ranged from a decadal to centennial time scale, varying with initial biomass type, pyrolysis temperature, and incubation or field study. The average turnover time using a one-pool approach was 88 y, and the best estimate using a two-pool approach was 3 y for a fast-cycling pool and 870 y for a slow-cycling pool. Based on this meta-analysis, PyC cannot be assumed to persist in soils for thousands of years, and its use as a strategy for offsetting carbon emissions requires prudence and further research.

Pyrolysis temperature and soil depth interactions determine PyC turnover and induced soil organic carbon priming

2021 ◽  
Vol 153 (1) ◽  
pp. 47-65
Author(s):  
Fernanda Santos ◽  
David M. Rice ◽  
Jeffrey A. Bird ◽  
Asmeret Asefaw Berhe
Keyword(s):  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Pyrolysis Temperature ◽  
Soil Depth

scholarly journals Freeze-Thaw Pretreatment Can Improve Efficiency of Bacterial DNA Extraction From Meconium

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuntian Xin ◽  
Jingxian Xie ◽  
Bingru Nan ◽  
Chen Tang ◽  
Yunshan Xiao ◽  
...  
Keyword(s):  
Species Diversity ◽  
Liquid Nitrogen ◽  
Dna Extraction ◽  
Extraction Efficiency ◽  
Bacterial Colonization ◽  
Care Hospital ◽  
Bacterial Dna ◽  
Freeze Thaw ◽  
Low Efficiency ◽  
Bacterial Dna Extraction

Although the presence of live microbes in utero remains under debate, newborn gastrointestinal bacteria are undoubtedly important to infant health. Measuring bacteria in meconium is an ideal strategy to understand this issue; however, the low efficiency of bacterial DNA extraction from meconium has limited its utilization. This study aims to improve the efficiency of bacterial DNA extraction from meconium, which generally has low levels of microflora but high levels of PCR inhibitors in the viscous matrix. The research was approved by the ethical committee of the Xiamen Maternity and Child Health Care Hospital, Xiamen, China. All the mothers delivered naturally, and their newborns were healthy. Meconium samples passed by the newborns within 24 h were collected. Each sample was scraped off of a sterile diaper, transferred to a 5-ml sterile tube, and stored at −80°C. For the assay, a freeze-thawing sample preparation protocol was designed, in which a meconium-InhibitEX buffer mixture was intentionally frozen 1–3 times at −20°C, −80°C, and (or) in liquid nitrogen. Then, DNA was extracted using a commercial kit and sequenced by 16S rDNA to verify the enhanced bacterial DNA extraction efficiency. Ultimately, we observed the following: (1) About 30 mg lyophilized meconium was the optimal amount for DNA extraction. (2) Freezing treatment for 6 h improved DNA extraction at −20°C. (3) DNA extraction efficiency was significantly higher with the immediate thaw strategy than with gradient thawing at −20°C, −80°C, and in liquid nitrogen. (4) Among the conditions of −20°C, −80°C, and liquid nitrogen, −20°C was the best freezing condition for both improving DNA extraction efficiency and preserving microbial species diversity in meconium, while liquid nitrogen was the worst condition. (5) Three freeze-thaw cycles could markedly enhance DNA extraction efficiency and preserve the species diversity of meconium microflora. We developed a feasible freeze-thaw pretreatment protocol to improve the extraction of microbial DNA from meconium, which may be beneficial for newborn bacterial colonization studies.

scholarly journals Fire-derived organic carbon turnover in soils on a centennial scale

2011 ◽  
Vol 8 (6) ◽  
pp. 12179-12195
Author(s):  
N. Singh ◽  
S. Abiven ◽  
M. S. Torn ◽  
M. W. I. Schmidt
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Organic Carbon ◽  
Pyrolysis Temperature ◽  
Plant Biomass ◽  
Meta Analysis ◽  
Turnover Time ◽  
Carbon Turnover ◽  
Biomass Pyrolysis ◽  
Pyrogenic Carbon

Abstract. Pyrogenic Carbon (PyC), the residue of an incomplete combustion of plant biomass, is considered as a carbon (C) sink due to its assumed stability in soil. Our meta-analysis of studies on PyC degradation challenges the assumption that PyC persist in soil for several thousand years. The turnover time for PyC estimated here ranges from decadal to centennial time scales, and is not slower than decomposition of bulk Soil Organic Matter (SOM) and differs with initial biomass, pyrolysis temperature and climate. Thus, using PyC as a strategy for offsetting carbon emissions requires caution and further research.

scholarly journals Efficiency of chemical versus mechanical disruption methods of DNA extraction for the identification of oral Gram-positive and Gram-negative bacteria

2020 ◽  
Vol 48 (5) ◽  
pp. 030006052092559
Author(s):  
Xiaolan Li ◽  
Caroline J. Bosch-Tijhof ◽  
Xi Wei ◽  
Johannes J. de Soet ◽  
Wim Crielaard ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Extraction Efficiency ◽  
Bacterial Species ◽  
Gram Positive ◽  
Bacterial Dna ◽  
Bacterial Cultures ◽  
Dna Extraction Method ◽  
Mp Method ◽  
Bacterial Dna Extraction

Objective Clinical diagnostics often requires the detection of multiple bacterial species in limited clinical samples with a single DNA extraction method. This study aimed to compare the bacterial DNA extraction efficiency of two lysis methods automated with the MagNA-Pure LC instrument. The samples included five oral bacterial species (three Gram-positive and two Gram-negative) with or without human saliva background. Methods Genomic DNA (gDNA) was extracted from bacterial cultures by bead-beating lysis (BMP) or chemical lysis (MP), followed by automated purification and measurement by quantitative PCR. Results For pure bacterial cultures, the MP method yielded higher quantities of extracted DNA and a lower detection limit than the BMP method, except where the samples contained high numbers of Gram-positive bacteria. For bacterial cultures with a saliva background, no difference in gDNA extraction efficacy was observed between the two methods. Conclusions The efficiency of a bacterial DNA extraction method is not only affected by the bacterial cell wall structure but also by the sample milieu. The MP method provided superior gDNA extraction efficiency when the samples contained a single bacterial species, whereas either of the BMP and MP methods could be applied with similar efficiencies to samples containing multiple species of bacteria.

scholarly journals High-Efficiency DNA Extraction Using Poly(4,4′-Cyclohexylidene Bisphenol Oxalate)-Modified Microcrystalline Cellulose-Magnetite Composite

2019 ◽  
Vol 2019 ◽  
pp. 1-10
Author(s):  
Aisha Nawaf Al balawi ◽  
Nor Azah Yusof ◽  
Sazlinda Kamaruzaman ◽  
Faruq Mohammad ◽  
Helmi Wasoh ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Microcrystalline Cellulose ◽  
High Efficiency ◽  
Extraction Efficiency ◽  
Total Yield ◽  
Polymer Surface ◽  
Magnetic Iron Oxide Nanoparticles ◽  
Composite Formation ◽  
Magnetite Particles ◽  
Phosphate Buffered Saline

In this study, we studied the DNA extraction capability of poly(4,4′-cyclohexylidene bisphenol oxalate) following the surface modification and composite formation with that of microcrystalline cellulose (MCC) and magnetic iron oxide nanoparticles (NPs). The physical characterization techniques like scanning electron microscopy (SEM), Fourier-transform infrared (FTIR) spectroscopy, energy-dispersive X-ray analysis (EDX), and thermogravimetric analysis (TGA) were employed for the poly(bisphenol Z oxalate)-MCC-magnetite composite during different stages of its formation. The results confirmed the successful modification of the polymer surface. On testing in the presence of three types of binding buffers, a high value of 72.4% (out of 10,000 ng/μL) efficiency with a total yield of DNA at 2×106 ng and absorbance ratio of A260/A280 (1.980) was observed for the 2 M GuHCl/EtOH binding buffer. These results were compared against the other two buffers of phosphate-buffered saline (PBS) and NaCl. The lowest value of DNA extraction efficiency at 8125 ng/μL of 58.845% with absorbance ratios of A260/A280 (1.818) for PBS was also observed. The study has concluded an enhancement in the DNA extraction efficiency when the polymer is in the composite stage along with cellulose and magnetite particles as compared against the bare polymer.

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